Network-Based Microbial Compositions and Methods

ABSTRACT

Provided are therapeutic compositions containing combinations of bacteria, for the maintenance or restoration of a healthy microbiota in the gastrointestinal tract of a mammalian subject, and methods for use thereof.

RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 14/777,252, filed Sep. 15, 2015, which is the National Stage of International Application No. PCT/US2014/030817, filed Mar. 17, 2014, which_claims the benefit of U.S. Provisional Application No. 61/798,666, filed Mar. 15, 2013, all of which are incorporated by reference in their entirety.

REFERENCE TO A SEQUENCE LISTING

This application includes a Sequence Listing submitted electronically as a text file named 40681_US_sequencelisting.txt, created on May 21, 2018, with a size of 4,166,333 bytes. The sequence listing is incorporated by reference.

BACKGROUND

Mammals are colonized by microbes in the gastrointestinal (GI) tract, on the skin, and in other epithelial and tissue niches such as the oral cavity, eye surface and vagina. The gastrointestinal tract harbors an abundant and diverse microbial community. It is a complex system, providing an environment or niche for a community of many different species or organisms, including diverse strains of bacteria. Hundreds of different species can form a commensal community in the GI tract in a healthy person, and this complement of organisms evolves from birth to ultimately form a functionally mature microbial population by about 3 years of age. Interactions between microbial strains in these populations and between microbes and the host (e.g. the host immune system) shape the community structure, with availability of and competition for resources affecting the distribution of microbes. Such resources may be food, location and the availability of space to grow or a physical structure to which the microbe may attach. For example, the host's diet is involved in shaping the GI tract flora.

A healthy microbiota provides the host with multiple benefits, including colonization resistance to a broad spectrum of pathogens, essential nutrient biosynthesis and absorption, and immune stimulation that maintains a healthy gut epithelium and an appropriately controlled systemic immunity. In settings of dysbiosis' or disrupted symbiosis, microbiota functions can be lost or deranged, resulting in increased susceptibility to pathogens, altered metabolic profiles, or induction of proinflammatory signals that can result in local or systemic inflammation or autoimmunity. Thus, the intestinal microbiota plays a significant role in the pathogenesis of many diseases and disorders. Many of these diseases and disorders are chronic conditions that significantly decrease a subject's quality of life and can be ultimately fatal.

Manufacturers of probiotics have asserted that their preparations of bacteria promote mammalian health by preserving the natural microflora in the GI tract and reinforcing the normal controls on aberrant immune responses. See, e.g., U.S. Pat. No. 8,034,601. Probiotics, however, have been limited to a very narrow group of genera and a correspondingly limited number of species. As such, they do not adequately replace the missing natural microflora nor correct dysbioses of the GI tract in many situations.

Therefore, in response to the need for durable, efficient, and effective compositions and methods for prevention, diagnosis and/or treatment of prediabetes and diabetes by way of restoring or enhancing microbiota functions, we address these and other shortcomings of the prior art by providing compositions and methods for treating subjects.

SUMMARY OF THE INVENTION

Disclosed herein are methods for treating, preventing, or reducing the severity of a disorder selected from the group consisting of Clostridium difficile Associated Diarrhea (CDAD), Type 2 Diabetes, Obesity, Irritable Bowel Disease (IBD), colonization with a pathogen or pathobiont, and infection with a drug-resistant pathogen or pathobiont, comprising: administering to a mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria or the purified bacterial preparation capable of forming a network ecology selected from the group consisting of N262.S, N290.S, N284.S, N271.S, N282.S, N288.S, N302.S, N279.S, N310.S, N323.S, N331.S, N332.S, N301.S, N312.S, N339.S, N325.S, N340.S, N341.S, N346.S, N338.S, N336.S, N345.S, N355.S, N356.S, N343.S, N329.S, N361.S, N353.S, N381.S, N344.S, N352.S, N357.S, N358.S, N369.S, N372.S, N375.S, N380.S, N374.S, N377.S, N368.S, N370.S, N373.S, N376.S, N389.S, N394.S, N431.S, N434.S, N390.S, N397.S, N387.S, N440.S, N396.S, N399.S, N403.S, N414.S, N430.S, N432.S, N436.S, N437.S, N457.S, N545, N386.S, N402.S, N405.S, N415.S, N421.S, N422.S, N423.S, N458.S, N459.S, N493.S, N416.S, N439.S, N447.S, N490.S, N526, N429.S, N433.S, N448.S, N488.S, N508.S, N509.S, N510.S, N511.S, N408.S, N446.S, N451.S, N474.S, N520.S, N521.S, N535.S, N516.S, N463.S, N518.S, N586, N450.S, N465.S, N519.S, N537.S, N419.S, N468.S, N477.S, N514.S, N382.S, N460.S, N462.S, N512.S, N517.S, N523.S, N547.S, N548.S, N577.S, N581.S, N585.S, N616.S, N466.S, N469.S, N480.S, N482.S, N484.S, N515.S, N533.S, N709, N730, N478.S, N572.S, N400.S, N543.S, N582.S, N621.S, N689, N769, N481.S, N525.S, N528.S, N534.S, N574.S, N580.S, N590.S, N591.S, N597.S, N664, N693, N530.S, N687, N470.S, N529.S, N539.S, N546.S, N570.S, N579.S, N602.S, N614.S, N648.S, N652.S, N655.S, N672.S, N681.S, N690.S, N692.S, N698.S, N737.S, N738.S, N785, N841, N878, N880, N881, N987, N988, N996, N1061, N479.S, N538.S, N542.S, N578.S, N609.S, N611.S, N617.S, N666.S, N675.S, N682.S, N844, N845, N846, N852, N876, N982, N1008, N649.S, N657.S, N678.S, N686.S, N710.S, N522.S, N651.S, N653.S, N654.S, N680.S, N712.S, N792, N802, N804, N807, N849, N858, N859, N875, N885, N942, N961, N972, N1051, N587.S, N589.S, N612.S, N625.S, N656.S, N714.S, N779, N781, N828, N829, N860, N894, N925, N927, N935, N947, N983, N1023, N441.S, N584.S, N794, N788, N524.S, N604.S, N610.S, N623.S, N663.S, N669.S, N676.S, N703.S, N775.S, N777.S, N780.S, N817.S, N827.S, N836.S, N871.S, N874.S, N898.S, N907.S, N998.S, N1088, N1089, N660.S, N665.S, N667.S, N733.S, N734.S, N739.S, N741.S, N782.S, N789.S, N796.S, N798.S, N800.S, N809.S, N816.S, N842.S, N843.S, N869.S, N986.S, N995.S, N1002.S, N1004.S, N1019.S, N1093, N668.S, N685.S, N835.S, N851.S, N464.S, N695.S, N776.S, N793.S, N815.S, N833.S, N891.S, N1070.S, N1092, N795.S, N797.S, N808.S, N811.S, N826.S, N830.S, N832.S, N840.S, N945.S, N960.S, N968.S, N1091, N805.S, N822.S, N928.S, N936.S, N1078.S, and N913.S.

In some embodiments, the therapeutic bacterial composition comprises at least one bacterial entity, wherein said bacterial entity is capable of forming the network ecology in combination with one more bacterial entities present in the gastrointestinal tract of the mammalian subject at the time of the administering or thereafter. In certain embodiments, the network ecology is selected from the group consisting of N1008, N1023, N1051, N1061, N1070.S, N1088, N1089, N1092, N381.S, N382.S, N387.S, N399.S, N400.S, N402.S, N403.S, N414.S, N429.S, N430.S, N432.S, N433.S, N436.S, N437.S, N439.S, N441.S, N447.S, N448.S, N457.S, N460.S, N462.S, N463.S, N464.S, N470.S, N474.S, N488.S, N490.S, N493.S, N508.S, N509.S, N510.S, N511.S, N512.S, N514.S, N515.S, N517.S, N518.S, N519.S, N520.S, N523.S, N524.S, N529.S, N539.S, N543.S, N546.S, N547.S, N548.S, N570.S, N574.S, N577.S, N579.S, N580.S, N582.S, N584.S, N585.S, N589.S, N591.S, N597.S, N602.S, N604.S, N609.S, N610.S, N611.S, N612.S, N614.S, N616.S, N621.S, N623.S, N625.S, N648.S, N651.S, N652.S, N653.S, N654.S, N655.S, N660.S, N663.S, N664, N665.S, N666.S, N669.S, N672.S, N676.S, N681.S, N687, N689, N690.S, N692.S, N693, N695.S, N698.S, N703.S, N709, N712.S, N714.S, N730, N734.S, N737.S, N738.S, N769, N775.S, N777.S, N779, N780.S, N781, N785, N788, N792, N793.S, N794, N797.S, N798.S, N802, N804, N807, N817.S, N827.S, N828, N830.S, N832.S, N833.S, N836.S, N840.S, N841, N844, N845, N849, N852, N858, N859, N860, N869.S, N871.S, N874.S, N875, N878, N880, N881, N885, N894, N898.S, N907.S, N913.S, N925, N927, N942, N947, N961, N968.S, N972, N982, N983, N986.S, N987, N988, N996, and N998.S.

In one embodiment, the network ecology consists essentially of N1008, N1023, N1051, N1061, N1070.S, N1088, N1089, N1092, N381.S, N382.S, N387.S, N399.S, N400.S, N402.S, N403.S, N414.S, N429.S, N430.S, N432.S, N433.S, N436.S, N437.S, N439.S, N441.S, N447.S, N448.S, N457.S, N460.S, N462.S, N463.S, N464.S, N470.S, N474.S, N488.S, N490.S, N493.S, N508.S, N509.S, N510.S, N511.S, N512.S, N514.S, N515.S, N517.S, N518.S, N519.S, N520.S, N523.S, N524.S, N529.S, N539.S, N543.S, N546.S, N547.S, N548.S, N570.S, N574.S, N577.S, N579.S, N580.S, N582.S, N584.S, N585.S, N589.S, N591.S, N597.S, N602.S, N604.S, N609.S, N610.S, N611.S, N612.S, N614.S, N616.S, N621.S, N623.S, N625.S, N648.S, N651.S, N652.S, N653.S, N654.S, N655.S, N660.S, N663.S, N664, N665.S, N666.S, N669.S, N672.S, N676.S, N681.S, N687, N689, N690.S, N692.S, N693, N695.S, N698.S, N703.S, N709, N712.S, N714.S, N730, N734.S, N737.S, N738.S, N769, N775.S, N777.S, N779, N780.S, N781, N785, N788, N792, N793.S, N794, N797.S, N798.S, N802, N804, N807, N817.S, N827.S, N828, N830.S, N832.S, N833.S, N836.S, N840.S, N841, N844, N845, N849, N852, N858, N859, N860, N869.S, N871.S, N874.S, N875, N878, N880, N881, N885, N894, N898.S, N907.S, N913.S, N925, N927, N942, N947, N961, N968.S, N972, N982, N983, N986.S, N987, N988, N996, or N998. S.

In another embodiment, the network ecology is selected from the group consisting of N387.S, N399.S, N512.S, N462.S, N651.S, N982, and N845. In one embodiment, network ecology comprises N387.S and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_262, clade_396, clade_444, clade_478, clade_500, and clade_553. In another embodiment, the network ecology comprises N387.S and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_262, clade_396, clade_444, clade_478, clade_500, and clade_553. In certain embodiments, clade_262 comprises one or more bacteria selected from the group consisting Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, wherein clade_396 comprises one or more bacteria selected from the group consisting Acetivibrio ethanolgignens, Anaerosporobacter mobilis, Bacteroides pectinophilus, Clostridium aminovalericum, Clostridium phytofermentans, Eubacterium hallii, and Eubacterium xylanophilum, wherein clade_444 comprises one or more bacteria selected from the group consisting Butyrivibrio fibrisolvens, Eubacterium rectale, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecalis, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, and Shuttleworthia sp. oral taxon G69, wherein clade_478 comprises one or more bacteria selected from the group consisting Faecalibacterium prausnitzii, Gemmiger formicilis, and Subdoligranulum variabile, wherein clade_500 comprises one or more bacteria selected from the group consisting Alistipes finegoldii, Alistipes onderdonkii, Alistipes putredinis, Alistipes shahii, Alistipes sp. HGB5, Alistipes sp. JC50, and Alistipes sp. RMA 9912, and wherein clade_553 comprises one or more bacteria selected from the group consisting Collinsella aerofaciens, Collinsella intestinalis, Collinsella stercoris, and Collinsella tanakaei.

In one embodiment, clade_262 comprises one or more bacteria of Ruminococcus torques, wherein clade_396 comprises one or more bacteria of Eubacterium hallii, wherein clade_444 comprises one or more bacteria selected from the group consisting of Eubacterium rectale and Roseburia inulinivorans, wherein clade_478 comprises one or more bacteria of Faecalibacterium prausnitzii, wherein clade_500 comprises one or more bacteria of Alistipes putredinis, and wherein clade_553 comprises one or more bacteria of Collinsella aerofaciens.

In another embodiment, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875, wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932, wherein clade_500 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 129, Seq. ID No.: 131, Seq. ID No.: 132, Seq. ID No.: 133, Seq. ID No.: 134, Seq. ID No.: 135, and Seq. ID No.: 136, and wherein clade_553 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 659, Seq. ID No.: 660, Seq. ID No.: 661, and Seq. ID No.: 662.

In other embodiments, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875, wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932, wherein clade_500 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 129, Seq. ID No.: 131, Seq. ID No.: 132, Seq. ID No.: 133, Seq. ID No.: 134, Seq. ID No.: 135, and Seq. ID No.: 136, and wherein clade_553 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 659, Seq. ID No.: 660, Seq. ID No.: 661, and Seq. ID No.: 662.

In one embodiment, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1670, wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 848, wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1639 and Seq. ID No.: 856, wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 880, wherein clade_500 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 132, and wherein clade_553 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 659.

In other embodiments, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1670, wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 848, wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1639 and Seq. ID No.: 856, wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 880, wherein clade_500 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 132, and wherein clade_553 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 659.

In another embodiment, network ecology comprises N399.S and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_262, clade_360, clade_396, clade_444, clade_478, and clade_494. In yet another embodiment, the network ecology comprises N399.S and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_262, clade_360, clade_396, clade_444, clade_478, and clade_494.

In some embodiments, clade_262 comprises one or more bacteria selected from the group consisting of Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, wherein clade_360 comprises one or more bacteria selected from the group consisting of Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, and Ruminococcus sp. ID8, wherein clade_396 comprises one or more bacteria selected from the group consisting of Acetivibrio ethanolgignens, Anaerosporobacter mobilis, Bacteroides pectinophilus, Clostridium aminovalericum, Clostridium phytofermentans, Eubacterium hallii, and Eubacterium xylanophilum, wherein clade_444 comprises one or more bacteria selected from the group consisting of Butyrivibrio fibrisolvens, Eubacterium rectale, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecalis, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, and Shuttleworthia sp. oral taxon G69, wherein clade_478 comprises one or more bacteria selected from the group consisting of Faecalibacterium prausnitzii, Gemmiger formicilis, and Subdoligranulum variabile, and wherein clade_494 comprises one or more bacteria selected from the group consisting of Clostridium orbiscindens, Clostridium sp. NML 04A032, Flavonifractor plautii, Pseudoflavonifractor capillosus, and Ruminococcaceae bacterium D16.

In another embodiment, clade_262 comprises one or more bacteria of Ruminococcus torques, wherein clade_360 comprises one or more bacteria of Dorea longicatena, wherein clade_396 comprises one or more bacteria of Eubacterium hallii, wherein clade_444 comprises one or more bacteria of Eubacterium rectale, wherein clade_478 comprises one or more bacteria of Faecalibacterium prausnitzii, and wherein clade_494 comprises one or more bacteria of Pseudoflavonifractor capillosus.

In one embodiment, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875, wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932, and wherein clade_494 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1591, Seq. ID No.: 1655, Seq. ID No.: 609, Seq. ID No.: 637, and Seq. ID No.: 886.

In some embodiments, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875, wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932, and wherein clade_494 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1591, Seq. ID No.: 1655, Seq. ID No.: 609, Seq. ID No.: 637, and Seq. ID No.: 886.

In other embodiments, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1670, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 774, wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 848, wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 856, wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 880, and wherein clade_494 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1591.

In one aspect, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1670, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 774, wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 848, wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 856, wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 880, and wherein clade_494 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1591.

In another aspect, the network ecology comprises N462. S and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_262, clade_360, and clade_478. In yet another aspect, the network ecology comprises N462.S and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_262, clade_360, and clade_478.

In other aspects, clade_262 comprises one or more bacteria selected from the group consisting of Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, wherein clade_360 comprises one or more bacteria selected from the group consisting of Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, and Ruminococcus sp. ID8, and wherein clade_478 comprises one or more bacteria selected from the group consisting of Faecalibacterium prausnitzii, Gemmiger formicilis, and Subdoligranulum variabile.

In another aspect, clade_262 comprises one or more bacteria of Coprococcus comes, wherein clade_360 comprises one or more bacteria of Dorea longicatena, and wherein clade_478 comprises one or more bacteria selected from the group consisting Faecalibacterium prausnitzii and Subdoligranulum variabile.

In yet another aspect, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932.

In certain aspects, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_478 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1896, Seq. ID No.: 880, and Seq. ID No.: 932.

In another aspect, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 774, and wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1896 and Seq. ID No.: 880.

In other aspects, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 774, and wherein clade_478 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1896 and Seq. ID No.: 880.

In another embodiment, network ecology comprises N512.S and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_262, clade_360, and clade_444. In one embodiment, the network ecology comprises N512.S and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_262, clade_360, and clade_444.

In other embodiments, clade_262 comprises one or more bacteria selected from the group consisting of Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, wherein clade_360 comprises one or more bacteria selected from the group consisting of Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, and Ruminococcus sp. ID8, and wherein clade_444 comprises one or more bacteria selected from the group consisting of Butyrivibrio fibrisolvens, Eubacterium rectale, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecalis, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, and Shuttleworthia sp. oral taxon G69.

In certain embodiments, clade_262 comprises one or more bacteria selected from the group consisting of Coprococcus comes and Ruminococcus torques, wherein clade_360 comprises one or more bacteria of Dorea longicatena, and wherein clade_444 comprises one or more bacteria of Eubacterium rectale.

In one embodiment, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865.

In another embodiment, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865.

In certain embodiments, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1670 and Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 774, and wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 856.

In one aspect, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1670 and Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 774, and wherein clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 856.

In another aspect, the network ecology comprises N845 and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_262, clade_360, and clade_378. In certain aspects, the network ecology comprises N845 and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_262, clade_360, and clade_378.

In other aspects, clade_262 comprises one or more bacteria selected from the group consisting of Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, wherein clade_360 comprises one or more bacteria selected from the group consisting of Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, and Ruminococcus sp. ID8, and wherein clade_378 comprises one or more bacteria selected from the group consisting of Bacteroides barnesiae, Bacteroides coprocola, Bacteroides coprophilus, Bacteroides dorei, Bacteroides massiliensis, Bacteroides plebeius, Bacteroides sp. 3_1_33FAA, Bacteroides sp. 3_1_40A, Bacteroides sp. 4_3_47FAA, Bacteroides sp. 9_1_42FAA, Bacteroides sp. NB_8, and Bacteroides vulgatus.

In certain aspects, clade_262 comprises one or more bacteria of Coprococcus comes, wherein clade_360 comprises one or more bacteria of Dorea longicatena, and wherein clade_378 comprises one or more bacteria of Bacteroides dorei.

In another aspect, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_378 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 267, Seq. ID No.: 272, Seq. ID No.: 273, Seq. ID No.: 274, Seq. ID No.: 284, Seq. ID No.: 289, Seq. ID No.: 309, Seq. ID No.: 310, Seq. ID No.: 313, Seq. ID No.: 314, Seq. ID No.: 323, and Seq. ID No.: 331.

In certain aspects, clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, wherein clade_360 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1050, Seq. ID No.: 1051, Seq. ID No.: 1053, Seq. ID No.: 1058, Seq. ID No.: 1661, Seq. ID No.: 1668, Seq. ID No.: 773, and Seq. ID No.: 774, and wherein clade_378 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 267, Seq. ID No.: 272, Seq. ID No.: 273, Seq. ID No.: 274, Seq. ID No.: 284, Seq. ID No.: 289, Seq. ID No.: 309, Seq. ID No.: 310, Seq. ID No.: 313, Seq. ID No.: 314, Seq. ID No.: 323, and Seq. ID No.: 331.

In one embodiment, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 774, and wherein clade_378 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 274.

In another embodiment, clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 674, wherein clade_360 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 774, and wherein clade_378 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 274.

In some embodiments, the network ecology comprises N982 and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_172, clade_262, and clade_396. In another embodiment, the network ecology comprises N982 and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_172, clade_262, and clade_396.

In certain aspects, clade_172 comprises one or more bacteria selected from the group consisting of Bifidobacteriaceae genomo sp. C1, Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium animalis, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium gallicum, Bifidobacterium infantis, Bifidobacterium kashiwanohense, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum, Bifidobacterium scardovii, Bifidobacterium sp. HM2, Bifidobacterium sp. HMLN12, Bifidobacterium sp. M45, Bifidobacterium sp. MSX5B, Bifidobacterium sp. TM_7, and Bifidobacterium thermophilum, wherein clade_262 comprises one or more bacteria selected from the group consisting of Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, and Ruminococcus torques, and wherein clade_396 comprises one or more bacteria selected from the group consisting of Acetivibrio ethanolgignens, Anaerosporobacter mobilis, Bacteroides pectinophilus, Clostridium aminovalericum, Clostridium phytofermentans, Eubacterium hallii, and Eubacterium xylanophilum.

In another aspect, clade_172 comprises one or more bacteria of Bifidobacterium longum, wherein clade_262 comprises one or more bacteria of Coprococcus comes, and wherein clade_396 comprises one or more bacteria of Eubacterium hallii.

In one aspect, clade_172 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 345, Seq. ID No.: 346, Seq. ID No.: 347, Seq. ID No.: 348, Seq. ID No.: 350, Seq. ID No.: 351, Seq. ID No.: 352, Seq. ID No.: 353, Seq. ID No.: 354, Seq. ID No.: 355, Seq. ID No.: 356, Seq. ID No.: 357, Seq. ID No.: 358, Seq. ID No.: 359, Seq. ID No.: 360, Seq. ID No.: 361, Seq. ID No.: 362, Seq. ID No.: 363, Seq. ID No.: 364, and Seq. ID No.: 365, wherein clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, and wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875.

In another aspect, clade_172 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 345, Seq. ID No.: 346, Seq. ID No.: 347, Seq. ID No.: 348, Seq. ID No.: 350, Seq. ID No.: 351, Seq. ID No.: 352, Seq. ID No.: 353, Seq. ID No.: 354, Seq. ID No.: 355, Seq. ID No.: 356, Seq. ID No.: 357, Seq. ID No.: 358, Seq. ID No.: 359, Seq. ID No.: 360, Seq. ID No.: 361, Seq. ID No.: 362, Seq. ID No.: 363, Seq. ID No.: 364, and Seq. ID No.: 365, wherein clade_262 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1048, Seq. ID No.: 1049, Seq. ID No.: 1057, Seq. ID No.: 1663, Seq. ID No.: 1670, Seq. ID No.: 588, Seq. ID No.: 607, and Seq. ID No.: 674, and wherein clade_396 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 161, Seq. ID No.: 288, Seq. ID No.: 551, Seq. ID No.: 6, Seq. ID No.: 613, Seq. ID No.: 848, and Seq. ID No.: 875.

In another aspect, clade_172 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 356, wherein clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 674, and wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 848.

In certain aspects, clade_172 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 356, wherein clade_262 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 674, and wherein clade_396 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 848.

In another embodiment, the network ecology comprises N651.S and the therapeutic bacterial composition comprises at least one bacterium selected from each of clade_444, clade_516, and clade_522. In yet another embodiment, the network ecology comprises N651.S and the therapeutic bacterial composition consists essentially of at least one bacterium selected from each of clade_444, clade_516, and clade_522.

In one embodiment, clade_444 comprises one or more bacteria selected from the group consisting of Butyrivibrio fibrisolvens, Eubacterium rectale, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecalis, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, and Shuttleworthia sp. oral taxon G69, wherein clade_516 comprises one or more bacteria selected from the group consisting of Anaerotruncus colihominis, Clostridium methylpentosum, Clostridium sp. YIT 12070, Hydrogenoanaerobacterium saccharovorans, Ruminococcus albus, and Ruminococcus flavefaciens, and wherein clade_522 comprises one or more bacteria selected from the group consisting of Bacteroides galacturonicus, Eubacterium eligens, Lachnospira multipara, Lachnospira pectinoschiza, and Lactobacillus rogosae. In another embodiment, clade_444 comprises one or more bacteria of Roseburia inulinivorans, wherein clade_516 comprises one or more bacteria of Anaerotruncus colihominis, and wherein clade_522 comprises one or more bacteria of Eubacterium eligens. In some embodiments, clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_516 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1005, Seq. ID No.: 164, Seq. ID No.: 1656, Seq. ID No.: 1660, Seq. ID No.: 606, and Seq. ID No.: 642, and wherein clade_522 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1046, Seq. ID No.: 1047, Seq. ID No.: 1114, Seq. ID No.: 280, and Seq. ID No.: 845.

In other embodiments, clade_444 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1045, Seq. ID No.: 1634, Seq. ID No.: 1635, Seq. ID No.: 1636, Seq. ID No.: 1637, Seq. ID No.: 1638, Seq. ID No.: 1639, Seq. ID No.: 1640, Seq. ID No.: 1641, Seq. ID No.: 1728, Seq. ID No.: 1729, Seq. ID No.: 1730, Seq. ID No.: 456, Seq. ID No.: 856, and Seq. ID No.: 865, wherein clade_516 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1005, Seq. ID No.: 164, Seq. ID No.: 1656, Seq. ID No.: 1660, Seq. ID No.: 606, and Seq. ID No.: 642, and wherein clade_522 comprises one more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1046, Seq. ID No.: 1047, Seq. ID No.: 1114, Seq. ID No.: 280, and Seq. ID No.: 845.

In one embodiment, clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 1639, wherein clade_516 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 164, and wherein clade_522 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences having 97% or greater identity to Seq. ID No.: 845.

In one aspect, clade_444 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 1639, wherein clade_516 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 164, and wherein clade_522 comprises one or more bacteria selected from the group consisting of bacteria having 16S sequences Seq. ID No.: 845.

In another aspect, the composition further comprises a pharmaceutically-acceptable excipient. In one aspect, the therapeutic bacterial composition is substantially depleted of a residual habitat product of a fecal material. In certain aspects, the composition is formulated for oral administration. In other embodiments, the composition is capable of inducing the formation of IgA, RegIII-gamma, IL-10, regulatory T cells, TGF-beta, alpha-defensin, beta-defensin, or an antimicrobial peptide in the mammalian subject. In another embodiment, the composition is comestible.

The invention provides a composition, comprising any of the compositions administered according to the methods described above. The invention also includes a dosage unit comprising predetermined ratios of the isolated bacteria present in the network ecology as described above.

The invention provides a method for producing short chain fatty acids (SCFA) within a mammalian subject, comprising:administering to said mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria of the purified bacterial preparation capable of forming one or a plurality of bacterial functional pathways, the one or plurality of bacterial functional pathways capable of forming a functional network ecology selected from the group consisting of N262.S, N290.S, N284.S, N271.S, N282.S, N288.S, N302.S, N279.S, N310.S, N323.S, N331.S, N332.S, N301.S, N312.S, N339.S, N325.S, N340.S, N341.S, N346.S, N338.S, N336.S, N345.S, N355.S, N356.S, N343.S, N329.S, N361.S, N353.S, N381.S, N344.S, N352.S, N357.S, N358.S, N369.S, N372.S, N375.S, N380.S, N374.S, N377.S, N368.S, N370.S, N373.S, N376.S, N389.S, N394.S, N431.S, N434.S, N390.S, N397.S, N387.S, N440.S, N396.S, N399.S, N403.S, N414.S, N430.S, N432.S, N436.S, N437.S, N457.S, N545, N386.S, N402.S, N405.S, N415.S, N421.S, N422.S, N423.S, N458.S, N459.S, N493.S, N416.S, N439.S, N447.S, N490.S, N526, N429.S, N433.S, N448.S, N488.S, N508.S, N509.S, N510.S, N511.S, N408.S, N446.S, N451.S, N474.S, N520.S, N521.S, N535.S, N516.S, N463.S, N518.S, N586, N450.S, N465.S, N519.S, N537.S, N419.S, N468.S, N477.S, N514.S, N382.S, N460.S, N462.S, N512.S, N517.S, N523.S, N547.S, N548.S, N577.S, N581.S, N585.S, N616.S, N466.S, N469.S, N480.S, N482.S, N484.S, N515.S, N533.S, N709, N730, N478.S, N572.S, N400.S, N543.S, N582.S, N621.S, N689, N769, N481.S, N525.S, N528.S, N534.S, N574.S, N580.S, N590.S, N591.S, N597.S, N664, N693, N530.S, N687, N470.S, N529.S, N539.S, N546.S, N570.S, N579.S, N602.S, N614.S, N648.S, N652.S, N655.S, N672.S, N681.S, N690.S, N692.S, N698.S, N737.S, N738.S, N785, N841, N878, N880, N881, N987, N988, N996, N1061, N479.S, N538.S, N542.S, N578.S, N609.S, N611.S, N617.S, N666.S, N675.S, N682.S, N844, N845, N846, N852, N876, N982, N1008, N649.S, N657.S, N678.S, N686.S, N710.S, N522.S, N651.S, N653.S, N654.S, N680.S, N712.S, N792, N802, N804, N807, N849, N858, N859, N875, N885, N942, N961, N972, N1051, N587.S, N589.S, N612.S, N625.S, N656.S, N714.S, N779, N781, N828, N829, N860, N894, N925, N927, N935, N947, N983, N1023, N441.S, N584.S, N794, N788, N524.S, N604.S, N610.S, N623.S, N663.S, N669.S, N676.S, N703.S, N775.S, N777.S, N780.S, N817.S, N827.S, N836.S, N871.S, N874.S, N898.S, N907.S, N998.S, N1088, N1089, N660.S, N665.S, N667.S, N733.S, N734.S, N739.S, N741.S, N782.S, N789.S, N796.S, N798.S, N800.S, N809.S, N816.S, N842.S, N843.S, N869.S, N986.S, N995.S, N1002.S, N1004.S, N1019.S, N1093, N668.S, N685.S, N835.S, N851.S, N464.S, N695.S, N776.S, N793.S, N815.S, N833.S, N891.S, N1070.S, N1092, N795.S, N797.S, N808.S, N811.S, N826.S, N830.S, N832.S, N840.S, N945.S, N960.S, N968.S, N1091, N805.S, N822.S, N928.S, N936.S, N1078.S, and N913.S.

In one embodiment, the functional network ecology is selected from the group consisting of N1008, N1023, N1051, N1061, N1070.S, N1088, N1089, N1092, N381.S, N382.S, N399.S, N400.S, N402.S, N403.S, N414.S, N429.S, N430.S, N432.S, N433.S, N436.S, N437.S, N439.S, N441.S, N447.S, N448.S, N457.S, N460.S, N462.S, N463.S, N464.S, N470.S, N474.S, N488.S, N490.S, N493.S, N508.S, N509.S, N510.S, N511.S, N512.S, N514.S, N515.S, N517.S, N518.S, N519.S, N520.S, N523.S, N524.S, N528.S, N529.S, N539.S, N543.S, N546.S, N547.S, N548.S, N570.S, N574.S, N577.S, N579.S, N580.S, N582.S, N584.S, N585.S, N589.S, N591.S, N597.S, N602.S, N604.S, N609.S, N610.S, N611.S, N612.S, N614.S, N616.S, N621.S, N623.S, N625.S, N648.S, N651.S, N652.S, N653.S, N654.S, N655.S, N660.S, N663.S, N664, N665.S, N666.S, N669.S, N672.S, N676.S, N681.S, N687, N689, N690.S, N692.S, N693, N695.S, N698.S, N703.S, N709, N712.S, N714.S, N730, N734.S, N737.S, N738.S, N769, N775.S, N777.S, N779, N780.S, N781, N785, N788, N792, N793.S, N794, N797.S, N798.S, N802, N804, N807, N817.S, N827.S, N828, N830.S, N832.S, N833.S, N836.S, N840.S, N841, N844, N845, N849, N852, N858, N859, N860, N869.S, N871.S, N874.S, N875, N878, N880, N881, N885, N894, N898.S, N907.S, N913.S, N925, N927, N942, N947, N961, N968.S, N972, N982, N983, N986.S, N987, N988, N996, and N998.S. In another embodiment, the functional network ecology is N528.S, and the plurality of bacterial functional pathways comprises the functional pathways of of KO:K00656, KO:K01069, KO:K01734, KO:K03417, KO:K03778, KO:K07246.

The invention includes a method for catalyzing secondary metabolism of bile acids within a mammalian subject, comprising: administering to said mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria of the purified bacterial preparation capable of forming one or a plurality of bacterial functional pathways, the one or plurality of bacterial functional pathways capable of forming a functional network ecology selected from the group consisting of N262.S, N290.S, N284.S, N271.S, N282.S, N288.S, N302.S, N279.S, N310.S, N323.S, N331.S, N332.S, N301.S, N312.S, N339.S, N325.S, N340.S, N341.S, N346.S, N338.S, N336.S, N345.S, N355.S, N356.S, N343.S, N329.S, N361.S, N353.S, N381.S, N344.S, N352.S, N357.S, N358.S, N369.S, N372.S, N375.S, N380.S, N374.S, N377.S, N368.S, N370.S, N373.S, N376.S, N389.S, N394.S, N431.S, N434.S, N390.S, N397.S, N387.S, N440.S, N396.S, N399.S, N403.S, N414.S, N430.S, N432.S, N436.S, N437.S, N457.S, N545, N386.S, N402.S, N405.S, N415.S, N421.S, N422.S, N423.S, N458.S, N459.S, N493.S, N416.S, N439.S, N447.S, N490.S, N526, N429.S, N433.S, N448.S, N488.S, N508.S, N509.S, N510.S, N511.S, N408.S, N446.S, N451.S, N474.S, N520.S, N521.S, N535.S, N516.S, N463.S, N518.S, N586, N450.S, N465.S, N519.S, N537.S, N419.S, N468.S, N477.S, N514.S, N382.S, N460.S, N462.S, N512.S, N517.S, N523.S, N547.S, N548.S, N577.S, N581.S, N585.S, N616.S, N466.S, N469.S, N480.S, N482.S, N484.S, N515.S, N533.S, N709, N730, N478.S, N572.S, N400.S, N543.S, N582.S, N621.S, N689, N769, N481.S, N525.S, N528.S, N534.S, N574.S, N580.S, N590.S, N591.S, N597.S, N664, N693, N530.S, N687, N470.S, N529.S, N539.S, N546.S, N570.S, N579.S, N602.S, N614.S, N648.S, N652.S, N655.S, N672.S, N681.S, N690.S, N692.S, N698.S, N737.S, N738.S, N785, N841, N878, N880, N881, N987, N988, N996, N1061, N479.S, N538.S, N542.S, N578.S, N609.S, N611.S, N617.S, N666.S, N675.S, N682.S, N844, N845, N846, N852, N876, N982, N1008, N649.S, N657.S, N678.S, N686.S, N710.S, N522.S, N651.S, N653.S, N654.S, N680.S, N712.S, N792, N802, N804, N807, N849, N858, N859, N875, N885, N942, N961, N972, N1051, N587.S, N589.S, N612.S, N625.S, N656.S, N714.S, N779, N781, N828, N829, N860, N894, N925, N927, N935, N947, N983, N1023, N441.S, N584.S, N794, N788, N524.S, N604.S, N610.S, N623.S, N663.S, N669.S, N676.S, N703.S, N775.S, N777.S, N780.S, N817.S, N827.S, N836.S, N871.S, N874.S, N898.S, N907.S, N998.S, N1088, N1089, N660.S, N665.S, N667.S, N733.S, N734.S, N739.S, N741.S, N782.S, N789.S, N796.S, N798.S, N800.S, N809.S, N816.S, N842.S, N843.S, N869.S, N986.S, N995.S, N1002.S, N1004.S, N1019.S, N1093, N668.S, N685.S, N835.S, N851.S, N464.S, N695.S, N776.S, N793.S, N815.S, N833.S, N891.S, N1070.S, N1092, N795.S, N797.S, N808.S, N811.S, N826.S, N830.S, N832.S, N840.S, N945.S, N960.S, N968.S, N1091, N805.S, N822. S, N928. S, N936. S, N1078. S, and N913. S.

In one embodiment, the functional network ecology is selected from the group consisting of N1008, N1023, N1051, N1061, N1070.S, N1088, N1089, N1092, N381.S, N382.S, N399.S, N400.S, N402.S, N403.S, N414.S, N429.S, N430.S, N432.S, N433.S, N436.S, N437.S, N439.S, N441.S, N447.S, N448.S, N457.S, N460.S, N462.S, N463.S, N464.S, N470.S, N474.S, N488.S, N490.S, N493.S, N508.S, N509.S, N510.S, N511.S, N512.S, N514.S, N515.S, N517.S, N518.S, N519.S, N520.S, N523.S, N524.S, N529.S, N539.S, N543.S, N546.S, N547.S, N548.S, N570.S, N574.S, N577.S, N579.S, N580.S, N582.S, N584.S, N585.S, N589.S, N591.S, N597.S, N602.S, N604.S, N609.S, N610.S, N611.S, N612.S, N614.S, N616.S, N621.S, N623.S, N625.S, N648.S, N651.S, N652.S, N653.S, N654.S, N655.S, N660.S, N663.S, N664, N665.S, N666.S, N669.S, N672.S, N676.S, N681.S, N687, N689, N690.S, N692.S, N693, N695.S, N698.S, N703.S, N709, N712.S, N714.S, N730, N734.S, N737.S, N738.S, N769, N775.S, N777.S, N779, N780.S, N781, N785, N788, N792, N793.S, N794, N797.S, N798.S, N802, N804, N807, N817.S, N827.S, N828, N830.S, N832.S, N833.S, N836.S, N840.S, N841, N844, N845, N849, N852, N858, N859, N860, N869.S, N871.S, N874.S, N875, N878, N880, N881, N885, N894, N898.S, N907.S, N913.S, N925, N927, N942, N947, N961, N968.S, N972, N982, N983, N986.S, N987, N988, N996, and N998.S. In another embodiment, the functional network ecology is N660.S and the plurality of bacterial functional pathways comprises the functional pathways of of KO:K00656, and KO:K01442.

In some embodiment, the invention includes a composition further comprising a pharmaceutically-acceptable excipient. In one embodiment, the composition is formulated for oral administration. In another embodiment, the composition is capable of inducing the formation of butyrate, propionate, acetate, 7-deoxybile acids, deoxycholate acide (DCA) and lithocholic acid (LCA) in the mammalian subject. In other embodiments, the composition is capable of inducing the depletion of glucose, pyruvate, lactate, cellulose, fructans, starch, xylans, pectins, taurocholate, glycocholate, ursocholate, cholate, glycochenodeoxycholate, taurochenodeoxycholate, ursodeoxycholate, or chenodeoxycholate; or the formation and depletion of intermediary metabolites acetyl-CoA, butyryl-CoA, propanoyl-CoA, chenodeoxycholoyl-CoA, or ursodeoxycholoyl-CoA in the mammalian subject. In another embodiment, the composition is formulated with one or more prebiotic compounds. In some embodiments, the composition is comestible.

The invention includes a composition, comprising any of the compositions administered according to the methods described above.

The invention also includes a dosage unit comprising predetermined ratios of the isolated bacteria present in the network ecology described above.

The invention comprises a pharmaceutical formulation comprising a purified bacterial population consisting essentially of a bacterial network capable of forming germinable bacterial spores, wherein the bacterial network is present in an amount effective to populate the gastrointestinal tract in a mammalian subject in need thereof to whom the formulation is administered, under conditions such that at least one type of bacteria not detectably present in the bacterial network or in the gastrointestinal tract prior to administration is augmented.

The invention also includes a pharmaceutical formulation comprising a purified bacterial population comprising a plurality of bacterial entities, wherein the bacterial entities are present in an amount effective to induce the formation of a functional bacterial network in the gastrointestinal tract in a mammalian subject in need thereof to whom the formulation is administered. In some embodiments, the functional bacterial network comprises bacterial entities present in the formulation. In other embodiments, the functional bacterial network comprises bacterial entities present in the gastrointestinal tract at the time of administration. In another embodiment, the functional bacterial network comprises bacterial entities not present in the formulation or the gastrointestinal tract at the time of administration. In one embodiment, the formulation can be provided as an oral finished pharmaceutical dosage form including at least one pharmaceutically acceptable carrier In some embodiments, the formulation of claim 83 or claim 84, wherein the mammalian subject suffers from a dysbiosis comprising a gastrointestinal disease, disorder or condition selected from the group consisting of Clostridium difficile Associated Diarrhea (CDAD), Type 2 Diabetes, Type 1 Diabetes, Obesity, Irritable Bowel Syndrome (IBS), Irritable Bowel Disease (IBD), Ulcerative Colitis, Crohn's Disease, colitis, colonization with a pathogen or pathobiont, and infection with a drug-resistant pathogen or pathobiont.

In another embodiment, the bacterial network is purified from a fecal material subjected to a treatment step that comprises depleting or inactivating a pathogenic material. In one embodiment, the bacterial network is substantially depleted of a detectable level of a first pathogenic material. In some embodiments, the bacterial network is substantially depleted of a residual habitat product of the fecal material.

In one embodiment, the invention provides a method of treating or preventing a dysbiosis in a human subject, comprising administering to the human subject the formulation of claim 83 or claim 84 in an amount effective to treat or prevent a dysbiosis or to reduce the severity of at least one symptom of the dysbiosis in the human subject to whom the formulation is administered.

In another embodiment, the formulation is provided as an oral finished pharmaceutical dosage form including at least one pharmaceutically acceptable carrier, the dosage form comprising at least about 1×10⁴ colony forming units of bacterial spores per dose of the composition, wherein the bacterial spores comprise at least two bacterial entities comprising 16S rRNA sequences at least 97% identical to the nucleic acid sequences selected from the group consisting of Seq. ID No.: 674, Seq. ID No.: 1670, Seq. ID No.: 774, Seq. ID No.: 848, Seq. ID No.: 856, Seq. ID No.: 1639, Seq. ID No.: 880, Seq. ID No.: 1896, Seq. ID No.: 1591, Seq. ID No.: 164, Seq. ID No.: 845, and Seq. ID No.: 659.

In yet another embodiment, the administration of the formulation results in a reduction or an elimination of at least one pathogen and/or pathobiont present in the gastrointestinal tract when the therapeutic composition is administered. In one embodiment, the administration of the formulation results in engraftment of at least one type of spore-forming bacteria present in the therapeutic composition.

In one aspect, the administration of the formulation results in augmentation in the gastrointestinal tract of the subject to whom the formulation is administered of at least one type of bacteria not present in the formulation. In another aspect, the at least one type of spore-forming bacteria are not detectably present in the gastrointestinal tract of the subject to whom the formulation is administered when the formulation is administered. In yet another aspect, the administration of the formulation results in at least two of: i) reduction or elimination of at least one pathogen and/or pathobiont present in the gastrointestinal tract when the formulation is administered; ii) engraftment of at least one type of spore-forming bacteria present in the therapeutic composition; and iii) augmentation of at least one type of spore-forming or non-spore forming bacteria not present in the therapeutic composition.

In some aspects, the administration of the therapeutic composition results in at reduction or elimination of at least one pathogen and/or pathobiont present in the gastrointestinal tract when the therapeutic composition is administered and at least one of: i) engraftment of at least one type of spore-forming bacteria present in the therapeutic composition; and ii) augmentation of at least one type of bacteria not present in the therapeutic composition.

In another aspect, the method of inducing engraftment of a bacterial population in the gastrointestinal tract of a human subject, comprising the step of administering to the human subject an orally acceptable pharmaceutical formulation comprising a purified bacterial network, under conditions such that at least i) a subset of the spore-forming bacteria sustainably engraft within the gastrointestinal tract, or ii) at least one type of bacteria not present in the therapeutic composition is augmented within the gastrointestinal tract.

The invention provides a pharmaceutical formulation comprising a purified first bacterial entity and a purified second bacterial entity, wherein the first bacterial entity comprises a first nucleic acid sequence encoding a first polypeptide capable of catalyzing a first chemical reaction, wherein the second bacterial entity comprises a second nucleic acid sequence encoding a second polypeptide capable of catalyzing a second chemical reaction, wherein the pharmaceutical formulation is formulated for oral administration to a mammalian subject in need thereof, wherein the first chemical reaction and the second chemical reaction are capable of occurring in the gastrointestinal tract of the mammalian subject under conditions such that a first product of the first chemical reaction, a substance present within said mammalian subject, or a combination of said first product with the substance is used as a substrate in the second chemical reaction to form a second product, wherein the second product induces a host cell response. In one embodiment, the substance is a mammalian subject protein or a food-derived protein. In another embodiment, the host cell response comprises production by the host cell of a biological material. In certain embodiments, the biological material comprises a cytokine, growth factor or signaling polypeptide.

In one embodiment, the host cell response comprises an immune response. In another embodiment, the host cell response comprises decreased gastric motility. In yet another embodiment, the host cell response comprises change in host gene expression, increased host metabolism, reduced gut permeability, enhanced epithelial cell junction integrity, reduced lipolysis by the action of Lipoprotein Lipase in adipose tissue, decreased hepatic gluconeogenesis, increased insulin sensitivity, increased production of FGF-19, or change in energy harvesting and/or storage.

The invention includes a pharmaceutical formulation comprising a purified first bacterial entity and a purified second bacterial entity, wherein the first bacterial entity and the second bacterial entity form a functional bacterial network in the gastrointestinal tract of a mammalian subject to whom the pharmaceutical formulation is administered, wherein the functional network modulates the level and/or activity of a biological material capable of inducing a host cell response.

The invention also includes a pharmaceutical formulation comprising a purified first bacterial entity and a purified second bacterial entity, wherein the first bacterial entity and the second bacterial entity form a functional bacterial network in the gastrointestinal tract of a mammalian subject to whom the pharmaceutical formulation is administered, wherein the functional network induces the production of a biological material capable of inducing a host cell response.

The invention comprises a therapeutic composition, comprising a network of at least two bacterial entities, wherein the network comprises at least one keystone bacterial entity and at least one non-keystone bacterial entity, wherein the at least two bacterial entities are each provided in amounts effective for the treatment or prevention of a gastrointestinal disease, disorder or condition in a mammalian subject. In one aspect, the network comprises at least three bacterial entities. In another aspect, the network comprises at least three bacterial entities including at least two keystone bacterial entities.

The invention comprises a therapeutic composition, comprising a network of at least two keystone bacterial entities capable of forming germination-competent spores, wherein the at least two keystone bacterial entities are each provided in amounts effective for the treatment or prevention of a gastrointestinal disease, disorder or condition in a mammalian subject. In one aspect, the comprision comprises a network of at least two keystone bacterial entities capable of forming germination-competent spores.

In one embodiment, the invention comprises a therapeutic composition, comprising: a first network of at least two bacterial entities, wherein the first network comprises a keystone bacterial entity and a non-keystone bacterial entity; and a second network of at least two bacterial entities, wherein the second network comprises at least one keystone bacterial entity and at least one non-keystone bacterial entity, wherein the networks are each provided in amounts effective for the treatment or prevention of a gastrointestinal disease, disorder or condition in a mammalian subject.

The invention includes a therapeutic composition, comprising a network of at least two bacterial entities, wherein the network comprises a first keystone bacterial entity and a second keystone bacterial entity, wherein the two bacterial entities are each provided in amounts effective for the treatment or prevention of a gastrointestinal disease, disorder or condition in a mammalian subject. In one aspect, the first and second keystone bacterial entities are present in the same network. In another aspect, the first and second keystone bacterial entities are present in different networks.

In some aspects, the invention comprises a diagnostic composition for the detection of a dysbiosis, comprising a first detection moiety capable of detecting a first keystone bacterial entity and a second detection moiety capable of detecting a first non-keystone bacterial entity, wherein the keystone bacterial entity and the non-keystone bacterial entity comprise a network, wherein the absence of at least one of the keystone bacterial entity and the non-keystone bacterial entity in a mammalian subject is indicative of a dysbiosis.

The invention comprises a method of altering a microbiome population present in a mammalian subject, comprising the steps of determining the presence of an incomplete network of bacterial entities in the gastrointestinal tract of the mammalian subject, and introducing to the gastrointestinal tract of the mammalian subject an effective amount of one or more supplemental bacterial entities not detectable in the gastrointestinal tract of the mammalian subject prior to such administration, under conditions such that the incomplete network is completed, thereby altering the microbiome population.

In one embodiment, the one or more supplemental bacterial entities become part of the incomplete network, thereby forming a complete network. In another embodiment, the one or more supplemental bacterial entities alter the microbiota of the mammalian subject such that one or more additional bacterial entities complete the incomplete network. In yet another embodiment, the one or more supplemental bacterial entities comprise a network.

The invention includes a method for detection and correction of a dysbiosis in a mammalian subject in need thereof, comprising the steps of: providing a fecal sample from the mammalian subject comprising a plurality of bacterial entities; contacting the fecal sample with a first detection moiety capable of detecting a first bacterial entity present in an network; detecting the absence of the first bacterial entity in the fecal sample, thereby detecting a dysbiosis in the mammalian subject; and administering to the mammalian subject a composition comprising an effective amount of the first bacterial entity. In one embodiment, the method includes confirming that the dysbiosis in the mammalian subject has been corrected.

The invention comprises a system for predicting a dysbiosis in a subject, the system comprising: a storage memory for storing a dataset associated with a sample obtained from the subject, wherein the dataset comprises content data for at least one network of bacterial entities; and a processor communicatively coupled to the storage memory for determining a score with an interpretation function wherein the score is predictive of dysbiosis in the subject.

The invention also comprises a kit for diagnosis of a state of dysbiosis in a mammalian subject in need thereof, comprising a plurality of detection means suitable for use in detecting (1) a first bacterial entity comprising a keystone bacterial entity and (2) a second bacterial entity, wherein the first and second bacterial entities comprise a functional network ecology.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides a schematic of 16S rRNA gene and denotes the coordinates of hypervariable regions 1-9 (V1-V9), according to an embodiment of the invention. Coordinates of V1-V9 are 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294, and 1435-1465 respectively, based on numbering using E. coli system of nomenclature defined by Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene (16S rRNA) from Escherichia coli, PNAS 75(10):4801-4805 (1978).

FIG. 2 highlights in bold the nucleotide sequences for each hypervariable region in the exemplary reference E. coli 16S sequence (SEQ ID NO: 2051) described by Brosius et al.

FIG. 3 provides the OTU and clade composition of networks tested in experiment SP-376, according to an embodiment of the invention.

FIG. 4 illustrates the results of a nutrient utilization assay with Clostridium difficile and potential competitors of the pathogen. A plus sign (+) indicates that it is a nutrient for the isolate tested. A minus sign (−) indicates that it is not a nutrient for the isolate tested.

FIG. 5 demonstrates the microbial diversity measured in the ethanol-treated spore treatment sample and patient pre- and post-treatment samples, according to an embodiment of the invention. Total microbial diversity is defined using the Chaol Alpha-Diversity Index and is measured at the same genomic sampling depths to confirm adequate and comparable sequence coverage of the target samples. The patient pretreatment (purple) harbored a microbiome that was significantly reduced in total diversity as compared to the ethanol-treated spore treatment (red) and patient post treatment at days 5 (blue), 14 (orange), and 25 (green).

FIG. 6 demonstrates how patient microbial ecology is shifted by treatment with an ethanol-treated spore treatment from a dysbiotic state to a state of health. Principal coordinates analysis based on the total diversity and structure of the microbiome (Bray Curtis Beta Diversity) of the patient pre- and post-treatment delineates that the combination of engraftment of the OTUs from the spore treatment and the augmentation of the patient microbial ecology leads to a microbial ecology that is distinct from both the pretreatment microbiome and the ecology of the ethanol-treated spore treatment.

FIG. 7 demonstrates the augmentation of Bacteroides species in patients treated with the spore population, according to an embodiment of the invention.

FIG. 8 shows species engrafting versus species augmenting in patients microbiomes after treatment with a bacterial composition such as but not limited to an ethanol-treated spore population, according to an embodiment of the invention. Relative abundance of species that engrafted or augmented as described were determined based on the number of 16S sequence reads. Each plot is from a different patient treated with the bacterial composition such as but not limited to an ethanol-treated spore population for recurrent C. difficile.

FIG. 9 shows a set of survival curves demonstrating efficacy of the ethanol enriched spore population in a mouse prophylaxis model of C. difficile, according to an embodiment of the invention.

FIG. 10 illustrates an in vivo hamster Clostridium difficile relapse prevention model to validate efficacy of ethanol-treated spores and ethanol treated, gradient purified spores, according to an embodiment of the invention.

FIG. 11 shows an in vivo hamster Clostridium difficile relapse prevention model to validate efficacy of network ecology bacterial composition, according to an embodiment of the invention.

FIG. 12 shows secondary bile acid metabolism KEGG Orthology Pathway and associated enzymatic gene products defined by EC numbers.

FIG. 13 shows Butyrate (a.k.a butanoate) production KEGG Orthology Pathway and associated enzymatic gene products defined by EC numbers.

FIG. 14 shows Propionate (a.k.a. propanoate) production KEGG Orthology Pathway and associated enzymatic gene products defined by EC numbers.

FIG. 15 shows Acetate production KEGG Orthology Pathway and associated enzymatic gene products defined by EC numbers.

FIG. 16 is an overview of a method to computationally derive network ecologies, according to an embodiment of the invention.

FIG. 17 is a schematic representation of how Keystone OTUs (nodes 2 and 4, shaded circles) are central members of many network ecologies that contain non-Keystone OTUs (nodes 1, 3, and 5-9). Distinct network ecologies include [node 2--node 7], [node--3--node 2--node--4], [node 2--node 4--node 5--node 6--node 7], [node 1--node 2--node 8--node 9], and [node--node 3].

FIG. 18 exemplifies a Derivation of Network Ecology Classes, according to an embodiment of the invention. Subsets of networks are selected for use in defining Network Classes based on key biological criteria. Hierarchical Network clusters are defined by the presence (white) and absence (blue) of OTUs and/or Functional Metabolic Pathways and Classes are defined as branches of the hierarchical clustering tree based on the topological overlap measure.

FIG. 19 shows phenotypes assigned to samples for the computational derivation of Network Ecologies that typify microbiome states of health (Hpost, Hdon, & Hgen) and states of disease (DdonF & DpreF). The composition of the microbiome of samples in different phenotypes can overlap with the intersections, defined by H, HD, D designations, having different biological meanings.

FIG. 20 shows an exemplary phylogenetic tree and the relationship of OTUs and Clades. A, B, C, D, and E represent OTUs, also known as leaves in the tree. Clade 1 comprises OTUs A and B, Clade 2 comprises OTUs C, D and E, and Clade 3 is a subset of Clade 2 comprising OTUs D and E. Nodes in a tree that define clades in the tree can be either statistically supported or not statistically supported. OTUs within a clade are more similar to each other than to OTUs in another clade and the robustness the clade assignment is denoted by the degree of statistical support for a node upstream of the OTUs in the clade.

FIG. 21 is a high-level block diagram illustrating an example of a computer for use as a server or a user device, in accordance with one embodiment.

The figures depict various embodiments of the present invention for purposes of illustration only. One skilled in the art will readily recognize from the following discussion that alternative embodiments of the structures and methods illustrated herein may be employed without departing from the principles of the invention described herein.

DETAILED DESCRIPTION Overview

Disclosed herein are therapeutic compositions containing combinations of bacteria for the prevention, control, and treatment of gastrointestinal diseases, and other disorders and conditions that result in or are caused by a dysbiotic microbiome in a niche of a host. Such indications include, but are not limited to Clostridium difficile associated diarrhea (CDAD), Type 2 Diabetes, Ulcerative colitis, as well as infection by antibiotic resistant bacteria such as Carbapenem resistant Klebsiella pneomoniae (CRKp) and Vancomycin Resistant Enterococcus (VRE). These compositions are advantageous in being suitable for safe administration to humans and other mammalian subjects and are efficacious in numerous gastrointestinal diseases, disorders and conditions and in general nutritional health. While bacterial compositions are known, these are generally single bacterial strains or combinations of bacteria that are combined without understanding the ecology formed by a consortium of bacterial organisms, resulting in poor efficacy, instability, substantial variability and lack of adequate safety.

The human body is an ecosystem in which the microbiota and the microbiome play a significant role in the basic healthy function of human systems (e.g. metabolic, immunological, and neurological). The microbiota and resulting microbiome comprise an ecology of microorganisms that co-exist within single subjects interacting with one another and their host (i.e., the mammalian subject) to form a dynamic unit with inherent biodiversity and functional characteristics. Within these networks of interacting microbes (i.e. ecologies), particular members can contribute more significantly than others; as such these members are also found in many different ecologies, and the loss of these microbes from the ecology can have a significant impact on the functional capabilities of the specific ecology. Robert Paine coined the concept “Keystone Species” in 1969 (see Paine R T. 1969. A note on trophic complexity and community stability. The American Naturalist 103: 91-93.) to describe the existence of such lynchpin species that are integral to a given ecosystem regardless of their abundance in the ecological community. Paine originally describe the role of the starfish Pisaster ochraceus in marine systems and since the concept has been experimentally validated in numerous ecosystems.

The present invention provides methods to define important network ecologies and functional network ecologies that occur in healthy and diseased subjects, and provides the compositional constituents of these network ecologies. The method enables the derivation of ecological modules (i.e. groups or networks of organisms and metabolic functions) within a broader ecology that can catalyze a change from a dysbiotic microbiome to one that represents a state of health. In another embodiment the methods enable the de novo construction of a network ecology based on desired biological characteristics, including functional characteristics, e.g. a functional network ecology. The methods further provide keystone species (i.e. operational taxonomic units, or OTUs) and keystone metabolic functions that are members of these microbial communities based on their ubiquitous appearance in many different networks. Importantly, this method is distinguished from previous computational approaches by being the first method to define actual network ecologies that are found in many healthy subjects. Network ecologies comprise consortia of bacterial OTUs (i.e. genera, species, or strains) that form coherent intact biological communities with defined phylogenetic and/or functional properties. In other words, the structure-function relationships contained within any Network Ecology possess an inherent biodiversity profile and resulting biological functional capabilities. The specific bacterial combinations and functional capabilities of the resulting microbiome are efficacious for the treatment or prevention of diseases, disorders and conditions of the gastrointestinal tract or for the treatment or prevention of systemic diseases, disorders and conditions that are influenced by the microbiota of the gastrointestinal tract. Further the network ecologies have a modularity to their structure and function with specific nodes (as example OTUs, phylogenetic clades, functional pathways) comprising a backbone of the network onto which different r-groups (as example OTUs, phylogenetic clades, functional pathways) can be incorporated to achieve specific biological properties of the network ecology. Network Ecologies defined in terms of functional modalities are referred to as Functional Network Ecologies.

The network ecologies provided herein are useful in settings where a microbial dysbiosis is occurring, given their capacities to achieve one or more of the following actions: i) disrupting the existing microbiota and/or microbiome; ii) establishing a new microbiota and/or microbiome; and (iii) stabilizing a functional microbiota and/or microbiome that supports health. Such network ecologies may be sustainably present upon introduction into a mammalian subject, or may be transiently present until such time as the functional microbiota and/or microbiome are re-established. In therapeutic settings, treatment with a consortium of microbial OTUs will change the microbiome of the treated host from a state of disease to a state of health. This change in the total diversity and composition can be mediated by both: (i) engraftment of OTUs that comprise the therapeutic composition into the host's ecology (Engrafted Ecology), and (ii) the establishment of OTUs that are not derived from the therapeutic composition, but for which the treatment with the therapeutic composition changes the environmental conditions such that these OTUs can establish. This Augmented Ecology is comprised of OTUs that were present at lower levels in the host pre-treatment or that were exogenously introduced from a source other than the therapeutic composition itself.

Provided herein are computational methods based at least in part on network theory (Proulx S R, Promislow D E L, Phillips P C. 2005. Network thinking in ecology and evolution. Trends in Ecology & Evolution 20: 345-353.), that delineate ecological and functional structures of a group of microorganisms based on the presence or absence of the specific OTUs (i.e. microbial orders, families, genera, species or strains) or functions inherent to those OTUs in a population of sampled mammalian subjects. Notably, these network ecologies and functional network ecologies are not simply inferred based on the clustering of OTUs according to binary co-occurrences computed from average relative abundances across a set of subject samples (See e.g. Faust K, Sathirapongsasuti J F, Izard J, Segata N, Gevers D, Raes J, and Huttenhower C. 2012. Microbial co-occurrence relationships in the human microbiome. PLoS Computational Bioliology 8: e1002606. Lozupone C, Faust K, Raes J, Faith J J, Frank D N, Zaneveld J, Gordon J I, and Knight R. 2012. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Research 22: 1974-1984), but instead the ecologies represent actual communities of bacterial OTUs that are computationally derived and explicitly exist as an ecological network within one or more subjects. Further, we provide methods by which to characterize the biological significance of a given ecological network in terms of its phylogenetic diversity, functional properties, and association with health or disease. The present invention delineates ecologies suitable for the treatment or prevention of diseases, disorders, and conditions of the gastrointestinal tract or which are distal to the gastrointestinal tract but caused or perpetuated by a dysbiosis of the gut microbiota.

Definitions

As used herein, the term “purified bacterial preparation” refers to a preparation that includes bacteria that have been separated from at least one associated substance found in a source material or any material associated with the bacteria in any process used to produce the preparation.

A “bacterial entity” includes one or more bacteria. Generally, a first bacterial entity is distinguishable from a second bacterial entity

As used herein, the term “formation” refers to synthesis or production.

As used herein, the term “inducing” means increasing the amount or activity of a given material as dictated by context.

As used herein, the term “depletion” refers to reduction in amount of.

As used herein, a “prebiotic” is a comestible food or beverage or ingredient thereof that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health. Prebiotics may include complex carbohydrates, amino acids, peptides, or other essential nutritional components for the survival of the bacterial composition. Prebiotics include, but are not limited to, amino acids, biotin, fructooligosaccharide, galactooligosaccharides, inulin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, and xylooligosaccharides.

As used herein, “predetermined ratios” refer to ratios determined or selected in advance.

As used herein, “germinable bacterial spores” are spores capable of forming vegetative cells under certain environmental conditions.

As used herein, “detectably present” refers to present in an amount that can be detected using assays provided herein or otherwise known in the art that exist as of the filing date.

As used herein, “augmented” refers to an increase in amount and/or localization within to a point where it becomes detectably present.

As used herein, a “fecal material” refers to a solid waste product of digested food and includes feces or bowel washes.

As used herein, a “host cell response” is a response produced by a cell comprising a host organism.

As used herein, a “mammalian subject protein” refers to a protein produced by a mammalian subject and encoded by the mammalian subject genome.

As used herein, the term “food-derived” refers to a protein found in a consumed food.

As used herein, the term “biological material” refers to a material produced by a biological organism.

As used herein, the term “detection moiety” refers to an assay component that functions to detect an analyte.

As used herein, the term “incomplete network” refers to a partial network that lacks the entire set of components needed to carry out one or more network functions.

As used herein, the term “supplemental” refers to something that is additional and non-identical.

As used herein, the term “Antioxidant” refers to, without limitation, any one or more of various substances such as beta-carotene (a vitamin A precursor), vitamin C, vitamin E, and selenium that inhibit oxidation or reactions promoted by Reactive Oxygen Species (“ROS”) and other radical and non-radical species. Additionally, antioxidants are molecules capable of slowing or preventing the oxidation of other molecules. Non-limiting examples of antioxidants include astaxanthin, carotenoids, coenzyme Q10 (“CoQ10”), flavonoids, glutathione, Goji (wolfberry), hesperidin, lactowolfberry, lignan, lutein, lycopene, polyphenols, selenium, vitamin A, vitamin C, vitamin E, zeaxanthin, or combinations thereof.

“Backbone Network Ecology” or simply “Backbone Network” or “Backbone” are compositions of microbes that form a foundational composition that can be built upon or subtracted from to optimize a Network Ecology or Functional Network Ecology to have specific biological characteristics or to comprise desired functional properties, respectively. Microbiome therapeutics can be comprised of these “Backbone Networks Ecologies” in their entirety, or the “Backbone Networks” can be modified by the addition or subtraction of “R-Groups” to give the network ecology desired characteristics and properties. “R-Groups” can be defined in multiple terms including, but not limited to: individual OTUs, individual or multiple OTUs derived from a specific phylogenetic clade or a desired phenotype such as the ability to form spores, or functional bacterial compositions that comprise. “Backbone Networks” can comprise a computationally derived Network Ecology in its entirety or can be subsets of the computed network that represent key nodes in the network that contributed to efficacy such as but not limited to a composition of Keystone OTUs. The number of organisms in the human gastrointestinal tract, as well as the diversity between healthy individuals, is indicative of the functional redundancy of a healthy gut microbiome ecology. See The Human Microbiome Consortia. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214. This redundancy makes it highly likely that non-obvious subsets of OTUs or functional pathways (i.e. “Backbone Networks”) are critical to maintaining states of health and or catalyzing a shift from a dysbiotic state to one of health. One way of exploiting this redundancy is through the substitution of OTUs that share a given clade (see below) or of adding members of a clade not found in the Backbone Network.

“Bacterial Composition” refers to a consortium of microbes comprising two or more OTUs. Backbone Network Ecologies, Functional Network Ecologies, Network Classes, and Core Ecologies are all types of bacterial compositions. A “Bacterial Composition” can also refer to a composition of enzymes that are derived from a microbe or multiple microbes. As used herein, Bacterial Composition includes a therapeutic microbial composition, a prophylactic microbial composition, a Spore Population, a Purified Spore Population, or ethanol treated spore population.

“Clade” refers to the OTUs or members of a phylogenetic tree that are downstream of a statistically valid node in a phylogenetic tree (FIG. 20). The clade comprises a set of terminal leaves in the phylogenetic tree (i.e. tips of the tree) that are a distinct monophyletic evolutionary unit and that share some extent of sequence similarity. Clades are hierarchical. In one embodiment, the node in a phylogenetic tree that is selected to define a clade is dependent on the level of resolution suitable for the underlying data used to compute the tree topology.

The “Colonization” of a host organism includes the non-transitory residence of a bacterium or other microscopic organism. As used herein, “reducing colonization” of a host subject's gastrointestinal tract (or any other microbiotal niche) by a pathogenic or non-pathogenic bacterium includes a reduction in the residence time of the bacterium the gastrointestinal tract as well as a reduction in the number (or concentration) of the bacterium in the gastrointestinal tract or adhered to the luminal surface of the gastrointestinal tract. The reduction in colonization can be permanent or occur during a transient period of time. Reductions of adherent pathogens can be demonstrated directly, e.g., by determining pathogenic burden in a biopsy sample, or reductions may be measured indirectly, e.g., by measuring the pathogenic burden in the stool of a mammalian host.

A “Combination” of two or more bacteria includes the physical co-existence of the two bacteria, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the two bacteria.

“Cytotoxic” activity of bacterium includes the ability to kill a bacterial cell, such as a pathogenic bacterial cell. A “cytostatic” activity or bacterium includes the ability to inhibit, partially or fully, growth, metabolism, and/or proliferation of a bacterial cell, such as a pathogenic bacterial cell. Cytotoxic activity may also apply to other cell types such as but not limited to Eukaryotic cells.

“Dysbiosis” refers to a state of the microbiota or microbiome of the gut or other body area, including mucosal or skin surfaces in which the normal diversity and/or function of the ecological network is disrupted. Any disruption from the preferred (e.g., ideal) state of the microbiota can be considered a dysbiosis, even if such dysbiosis does not result in a detectable decrease in health. This state of dysbiosis may be unhealthy, it may be unhealthy under only certain conditions, or it may prevent a subject from becoming healthier. Dysbiosis may be due to a decrease in diversity, the overgrowth of one or more pathogens or pathobionts, symbiotic organisms able to cause disease only when certain genetic and/or environmental conditions are present in a patient, or the shift to an ecological network that no longer provides a beneficial function to the host and therefore no longer promotes health.

“Ecological Niche” or simply “Niche” refers to the ecological space in which an organism or group of organisms occupies. Niche describes how an organism or population or organisms responds to the distribution of resources, physical parameters (e.g., host tissue space) and competitors (e.g., by growing when resources are abundant, and when predators, parasites and pathogens are scarce) and how it in turn alters those same factors (e.g., limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey).

“Germinant” is a material or composition or physical-chemical process capable of inducing vegetative growth of a bacterium that is in a dormant spore form, or group of bacteria in the spore form, either directly or indirectly in a host organism and/or in vitro.

“Inhibition” of a pathogen or non-pathogn encompasses the inhibition of any desired function or activity y the bacterial compositions of the present invention. Demonstrations of inhibition, such as decrease in the growth of a pathogenic bacterium or reduction in the level of colonization of a pathogenic bacterium are provided herein and otherwise recognized by one of ordinary skill in the art. Inhibition of a pathogenic or non-pathogenic bacterium's “growth” may include inhibiting the increase in size of the pathogenic or non-pathogenic bacterium and/or inhibiting the proliferation (or multiplication) of the pathogenic or non-pathogenic bacterium. Inhibition of colonization of a pathogenic or non-pathogenic bacterium may be demonstrated by measuring the amount or burden of a pathogen before and after a treatment. An “inhibition” or the act of “inhibiting” includes the total cessation and partial reduction of one or more activities of a pathogen, such as growth, proliferation, colonization, and function. Inhibition of function includes, for example, the inhibition of expression of pathogenic gene products such as a toxin or invasive pilus induced by the bacterial composition.

“Isolated” encompasses a bacterium or other entity or substance that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, purified, and/or manufactured by the hand of man. Isolated bacteria include those bacteria that are cultured, even if such cultures are not monocultures. Isolated bacteria may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated. In some embodiments, isolated bacteria are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to a bacterium or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. A bacterium or a bacterial population may be considered purified if it is isolated at or after production, such as from a material or environment containing the bacterium or bacterial population, or by passage through culture, and a purified bacterium or bacterial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “isolated.” In some embodiments, purified bacteria and bacterial populations are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. In the instance of bacterial compositions provided herein, the one or more bacterial types present in the composition can be independently purified from one or more other bacteria produced and/or present in the material or environment containing the bacterial type. Bacterial compositions and the bacterial components thereof are generally purified from residual habitat products.

“Keystone OTU” or “Keystone Function” refers to one or more OTUs or Functional Pathways (e.g. KEGG or COG pathways) that are common to many network ecologies or functional network ecologies and are members of networks that occur in many subjects (i.e. are pervasive). Due to the ubiquitous nature of Keystone OTUs and their associated Functions Pathways, they are central to the function of network ecologies in healthy subjects and are often missing or at reduced levels in subjects with disease. Keystone OTUs and their associated functions may exist in low, moderate, or high abundance in subjects. “Non-Keystone OTU” or “non-Keystone Function” refers to an OTU or Function that is observed in a Network Ecology or a Functional Network Ecology and is not a keystone OTU or Function.

“Microbiota” refers to the community of microorganisms that occur (sustainably or transiently) in and on an animal subject, typically a mammal such as a human, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses i.e., phage).

“Microbiome” refers to the genetic content of the communities of microbes that live in and on the human body, both sustainably and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e., phage)), wherein “genetic content” includes genomic DNA, RNA such as ribosomal RNA, the epigenome, plasmids, and all other types of genetic information.

“Microbial Carriage” or simply “Carriage” refers to the population of microbes inhabiting a niche within or on humans. Carriage is often defined in terms of relative abundance. For example, OTU1 comprises 60% of the total microbial carriage, meaning that OTU1 has a relative abundance of 60% compared to the other OTUs in the sample from which the measurement was made. Carriage is most often based on genomic sequencing data where the relative abundance or carriage of a single OTU or group of OTUs is defined by the number of sequencing reads that are assigned to that OTU/s relative to the total number of sequencing reads for the sample. Alternatively, Carriage may be measured using microbiological assays.

“Microbial Augmentation” or simply “augmentation” refers to the establishment or significant increase of a population of microbes that are (i) absent or undetectable (as determined by the use of standard genomic and microbiological techniques) from the administered therapeutic microbial composition, (ii) absent, undetectable, or present at low frequencies in the host niche (for example: gastrointestinal tract, skin, anterior-nares, or vagina) before the delivery of the microbial composition, and (iii) are found after the administration of the microbial composition or significantly increased, for instance 2-fold, 5-fold, 1×10², 1×10³, 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, or greater than 1×10⁸, in cases where they were present at low frequencies. The microbes that comprise an augmented ecology can be derived from exogenous sources such as food and the environment, or grow out from micro-niches within the host where they reside at low frequency. The administration of a bacterial microbial composition induces an environmental shift in the target niche that promotes favorable conditions for the growth of these commensal microbes. In the absence of treatment with a bacterial composition, the host can be constantly exposed to these microbes; however, sustained growth and the positive health effects associated with the stable population of increased levels of the microbes comprising the augmented ecology are not observed.

“Microbial Engraftment” or simply “engraftment” refers to the establishment of OTUs present in the bacterial composition in a target niche that are absent in the treated host prior to treatment. The microbes that comprise the engrafted ecology are found in the therapeutic microbial composition and establish as constituents of the host microbial ecology upon treatment. Engrafted OTUs can establish for a transient period of time, or demonstrate long-term stability in the microbial ecology that populates the host post treatment with a bacterial composition. The engrafted ecology can induce an environmental shift in the target niche that promotes favorable conditions for the growth of commensal microbes capable of catalyzing a shift from a dysbiotic ecology to one representative of a health state.

As used herein, the term “Minerals” is understood to include boron, calcium, chromium, copper, iodine, iron, magnesium, manganese, molybdenum, nickel, phosphorus, potassium, selenium, silicon, tin, vanadium, zinc, or combinations thereof.

“Network Ecology” refers to a consortium of clades or OTUs that co-occur in some number of subjects. As used herein, a “network” is defined mathematically by a graph delineating how specific nodes (i.e. clades or OTUs) and edges (connections between specific clades or OTUs) relate to one another to define the structural ecology of a consortium of clades or OTUs. Any given Network Ecology will possess inherent phylogenetic diversity and functional properties. A Network Ecology can also be defined in terms of its functional capabilities where for example the nodes would be comprised of elements such as, but not limited to, enzymes, clusters of orthologous groups (COGS; ncbi.nlm.nih.gov/books/NBK21090/), or KEGG Orthology Pathways (genome.jp/kegg/); these networks are referred to as a “Functional Network Ecology”. Functional Network Ecologies can be reduced to practice by defining the group of OTUs that together comprise the functions defined by the Functional Network Ecology.

“Network Class” and “Network Class Ecology” refer to a group of network ecologies that in general are computationally determined to comprise ecologies with similar phylogenetic and/or functional characteristics. A Network Class therefore contains important biological features, defined either phylogenetically or functionally, of a group (i.e., a cluster) of related network ecologies. One representation of a Network Class Ecology is a designed consortium of microbes, typically non-pathogenic bacteria, that represents core features of a set of phylogenetically or functionally related network ecologies seen in many different subjects. In many occurrences, a Network Class, while designed as described herein, exists as a Network Ecology observed in one or more subjects. Network Class ecologies are useful for reversing or reducing a dysbiosis in subjects where the underlying, related Network Ecology has been disrupted. Exemplary Network Classes are provided in Table 12 and examples of phylogenetic signature by family of Network Classes are given in Table 13.

To be free of “non-comestible products” means that a bacterial composition or other material provided herein does not have a substantial amount of a non-comestible product, e.g., a product or material that is inedible, harmful or otherwise undesired in a product suitable for administration, e.g., oral administration, to a human subject. Non-comestible products are often found in preparations of bacteria from the prior art.

“Operational taxonomic units” and “OTU” (or plural, “OTUs”) refer to a terminal leaf in a phylogenetic tree and is defined by a nucleic acid sequence, e.g., the entire genome, or a specific genetic sequence, and all sequences that share sequence identity to this nucleic acid sequence at the level of species. In some embodiments the specific genetic sequence may be the 16S sequence or a portion of the 16S sequence. In other embodiments, the entire genomes of two entities are sequenced and compared. In another embodiment, select regions such as multilocus sequence tags (MLST), specific genes, or sets of genes may be genetically compared. In 16S embodiments, OTUs that share ≥97% average nucleotide identity across the entire 16S or some variable region of the 16S are considered the same OTU. See e.g. Claesson M J, Wang Q, O'Sullivan O, Greene-Diniz R, Cole J R, Ross R P, and O'Toole P W. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. In embodiments involving the complete genome, MLSTs, specific genes, other than 16S, or sets of genes OTUs that share ≥95% average nucleotide identity are considered the same OTU. See e.g., Achtman M, and Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6: 431-440. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. OTUs are frequently defined by comparing sequences between organisms. Generally, sequences with less than 95% sequence identity are not considered to form part of the same OTU. OTUs may also be characterized by any combination of nucleotide markers or genes, in particular highly conserved genes (e.g., “house-keeping” genes), or a combination thereof. Such characterization employs, e.g., WGS data or a whole genome sequence.

Table 1 below shows a List of Operational Taxonomic Units (OTU) with taxonomic assignments made to Genus, Species, and Phylogenetic Clade. Clade membership of bacterial OTUs is based on 16S sequence data. Clades are defined based on the topology of a phylogenetic tree that is constructed from full-length 16S sequences using maximum likelihood methods familiar to individuals with ordinary skill in the art of phylogenetics. Clades are constructed to ensure that all OTUs in a given clade are: (i) within a specified number of bootstrap supported nodes from one another, and (ii) within 5% genetic similarity. OTUs that are within the same clade can be distinguished as genetically and phylogenetically distinct from OTUs in a different clade based on 16S-V4 sequence data, while OTUs falling within the same clade are closely related. OTUs falling within the same clade are evolutionarily closely related and may or may not be distinguishable from one another using 16S-V4 sequence data. Members of the same clade, due to their evolutionary relatedness, play similar functional roles in a microbial ecology such as that found in the human gut. Compositions substituting one species with another from the same clade are likely to have conserved ecological function and therefore are useful in the present invention. All OTUs are denoted as to their putative capacity to form spores and whether they are a Pathogen or Pathobiont (see Definitions for description of “Pathobiont”). NIAID Priority Pathogens are denoted as ‘Category-A’, ‘Category-B’, or ‘Category-C’, and Opportunistic Pathogens are denoted as ‘OP’. OTUs that are not pathogenic or for which their ability to exist as a pathogen is unknown are denoted as ‘N’. The ‘SEQ ID Number’ denotes the identifier of the OTU in the Sequence Listing File and ‘Public DB Accession’ denotes the identifier of the OTU in a public sequence repository.

“Pathobiont” refer to specific bacterial species found in healthy hosts that may trigger immune-mediated pathology and/or disease in response to certain genetic or environmental factors (Chow et al. 2011. Curr Op Immunol. Pathobionts of the intestinal microbiota and inflammatory disease. 23: 473-80). Thus, a pathobiont is an opportunistic microbe that is mechanistically distinct from an acquired infectious organism. Thus, the term “pathogen” includes both acquired infectious organisms and pathobionts.

“Pathogen”, “pathobiont” and “pathogenic” in reference to a bacterium or any other organism or entity that includes any such organism or entity that is capable of causing or affecting a disease, disorder or condition of a host organism containing the organism or entity, including but not limited to pre-diabetes, type 1 diabetes or type 2 diabetes.

“Phenotype” refers to a set of observable characteristics of an individual entity. As example an individual subject may have a phenotype of “health” or “disease”. Phenotypes describe the state of an entity and all entities within a phenotype share the same set of characteristics that describe the phenotype. The phenotype of an individual results in part, or in whole, from the interaction of the entity's genome and/or microbiome with the environment, especially including diet.

“Phylogenetic Diversity” is a biological characteristic that refers to the biodiversity present in a given Network Ecology or Network Class Ecology based on the OTUs that comprise the network. Phylogenetic diversity is a relative term, meaning that a Network Ecology or Network Class that is comparatively more phylogenetically diverse than another network contains a greater number of unique species, genera, and taxonomic families. Uniqueness of a species, genera, or taxonomic family is generally defined using a phylogenetic tree that represents the genetic diversity all species, genera, or taxonomic families relative to one another. In another embodiment phylogenetic diversity may be measured using the total branch length or average branch length of a phylogenetic tree. Phylogenetic Diversity may be optimized in a bacterial composition by including a wide range of biodiversity.

“Phylogenetic tree” refers to a graphical representation of the evolutionary relationships of one genetic sequence to another that is generated using a defined set of phylogenetic reconstruction algorithms (e.g. parsimony, maximum likelihood, or Bayesian). Nodes in the tree represent distinct ancestral sequences and the confidence of any node is provided by a bootstrap or Bayesian posterior probability, which measures branch uncertainty.

“Prediabetes” refers a condition in which blood glucose levels are higher than normal, but not high enough to be classified as diabetes. Individuals with pre-diabetes are at increased risk of developing type 2 diabetes within a decade. According to CDC, prediabetes can be diagnosed by fasting glucose levels between 100-125 mg/dL, 2 hour post-glucose load plasma glucose in oral glucose tolerance test (OGTT) between 140 and 199 mg/dL, or hemoglobin A1c test between 5.7%-6.4%.

“rDNA”, “rRNA”, “16S-rDNA”, “16S-rRNA”, “16S”, “16S sequencing”, “16S-NGS”, “18S”, “18S-rRNA”, “18S-rDNA”, “18S sequencing”, and “18S-NGS” refer to the nucleic acids that encode for the RNA subunits of the ribosome. rDNA refers to the gene that encodes the rRNA that comprises the RNA subunits. There are two RNA subunits in the ribosome termed the small subunit (SSU) and large subunit (LSU); the RNA genetic sequences (rRNA) of these subunits is related to the gene that encodes them (rDNA) by the genetic code. rDNA genes and their complementary RNA sequences are widely used for determination of the evolutionary relationships amount organisms as they are variable, yet sufficiently conserved to allow cross organism molecular comparisons. Typically 16S rDNA sequence (approximately 1542 nucleotides in length) of the 30S SSU is used for molecular-based taxonomic assignments of Prokaryotes and the 18S rDNA sequence (approximately 1869 nucleotides in length) of 40S SSU is used for Eukaryotes. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most bacteria.

“Residual habitat products” refers to material derived from the habitat for microbiota within or on a human or animal. For example, microbiota live in feces in the gastrointestinal tract, on the skin itself, in saliva, mucus of the respiratory tract, or secretions of the genitourinary tract (i.e., biological matter associated with the microbial community). Substantially free of residual habitat products means that the bacterial composition no longer contains the biological matter associated with the microbial environment on or in the human or animal subject and is 100% free, 99% free, 98% free, 97% free, 96% free, or 95% free of any contaminating biological matter associated with the microbial community. Residual habitat products can include abiotic materials (including undigested food) or it can include unwanted microorganisms. Substantially free of residual habitat products may also mean that the bacterial composition contains no detectable cells from a human or animal and that only microbial cells are detectable. In one embodiment, substantially free of residual habitat products may also mean that the bacterial composition contains no detectable viral (including bacterial viruses (i.e., phage)), fungal, mycoplasmal contaminants. In another embodiment, it means that fewer than 1×10-2%, 1×10-3%, 1×10-4%, 1×10-5%, 1×10-6%, 1×10-7%, 1×10-8 of the viable cells in the bacterial composition are human or animal, as compared to microbial cells. There are multiple ways to accomplish this degree of purity, none of which are limiting. Thus, contamination may be reduced by isolating desired constituents through multiple steps of streaking to single colonies on solid media until replicate (such as, but not limited to, two) streaks from serial single colonies have shown only a single colony morphology. Alternatively, reduction of contamination can be accomplished by multiple rounds of serial dilutions to single desired cells (e.g., a dilution of 10-8 or 10-9), such as through multiple 10-fold serial dilutions. This can further be confirmed by showing that multiple isolated colonies have similar cell shapes and Gram staining behavior. Other methods for confirming adequate purity include genetic analysis (e.g. PCR, DNA sequencing), serology and antigen analysis, enzymatic and metabolic analysis, and methods using instrumentation such as flow cytometry with reagents that distinguish desired constituents from contaminants.

“Spore” or a population of “spores” includes bacteria (or other single-celled organisms) that are generally viable, more resistant to environmental influences such as heat and bacteriocidal agents than vegetative forms of the same bacteria, and typically capable of germination and out-growth. Spores are characterized by the absence of active metabolism until they respond to specific environmental signals, causing them to germinate. “Spore-formers” or bacteria “capable of forming spores” are those bacteria containing the genes and other necessary abilities to produce spores under suitable environmental conditions. A Table of preferred spore-forming bacterial compositions is provided in Table 11.

“Spore population” refers to a plurality of spores present in a composition. Synonymous terms used herein include spore composition, spore preparation, ethanol-treated spore fraction and spore ecology. A spore population may be purified from a fecal donation, e.g. via ethanol or heat treatment, or a density gradient separation or any combination of methods described herein to increase the purity, potency and/or concentration of spores in a sample. Alternatively, a spore population may be derived through culture methods starting from isolated spore former species or spore former OTUs or from a mixture of such species, either in vegetative or spore form.

In one embodiment, the spore preparation comprises spore forming species wherein residual non-spore forming species have been inactivated by chemical or physical treatments including ethanol, detergent, heat, sonication, and the like; or wherein the non-spore forming species have been removed from the spore preparation by various separations steps including density gradients, centrifugation, filtration and/or chromatography; or wherein inactivation and separation methods are combined to make the spore preparation. In yet another embodiment, the spore preparation comprises spore forming species that are enriched over viable non-spore formers or vegetative forms of spore formers. In this embodiment, spores are enriched by 2-fold, 5-fold, 10-fold, 50-fold, 100-fold, 1000-fold, 10,000-fold or greater than 10,000-fold compared to all vegetative forms of bacteria. In yet another embodiment, the spores in the spore preparation undergo partial germination during processing and formulation such that the final composition comprises spores and vegetative bacteria derived from spore forming species.

“Sporulation induction agent” is a material or physical-chemical process that is capable of inducing sporulation in a bacterium, either directly or indirectly, in a host organism and/or in vitro.

To “increase production of bacterial spores” includes an activity or a sporulation induction agent. “Production” includes conversion of vegetative bacterial cells into spores and augmentation of the rate of such conversion, as well as decreasing the germination of bacteria in spore form, decreasing the rate of spore decay in vivo, or ex vivo, or to increasing the total output of spores (e.g. via an increase in volumetric output of fecal material).

“Subject” refers to any animal subject including humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs, turkeys, and chickens), and household pets (e.g., dogs, cats, and rodents). The subject may be suffering from a dysbiosis, that contributes to or causes a condition classified as diabetes or pre-diabetes, including but not limited to mechanisms such as metabolic endotoxemia, altered metabolism of primary bile acids, immune system activation, or an imbalance or reduced production of short chain fatty acids including butyrate, propionate, acetate, and branched chain fatty acids.

As used herein the term “Vitamin” is understood to include any of various fat-soluble or water-soluble organic substances (non-limiting examples include Vitamin A, Vitamin B1 (thiamine), Vitamin B2 (riboflavin), Vitamin B3 (niacin or niacinamide), Vitamin B5 (pantothenic acid), Vitamin B6 (pyridoxine, pyridoxal, or pyridoxamine, or pyridoxine hydrochloride), Vitamin B7 (biotin), Vitamin B9 (folic acid), and Vitamin B12 (various cobalamins; commonly cyanocobalamin in vitamin supplements), Vitamin C, Vitamin D, Vitamin E, Vitamin K, K1 and K2 (i.e., MK-4, MK-7), folic acid and biotin) essential in minute amounts for normal growth and activity of the body and obtained naturally from plant and animal foods or synthetically made, pro-vitamins, derivatives, analogs.

“V1-V9 regions” or “16S V1-V9 regions” refers to the 16S rRNA refers to the first through ninth hypervariable regions of the 16S rRNA gene that are used for genetic typing of bacterial samples. These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805 (1978). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU. A person of ordinary skill in the art can identify the specific hypervariable regions of a candidate 16S rRNA by comparing the candidate sequence in question to a reference sequence and identifying the hypervariable regions based on similarity to the reference hypervariable regions, or alternatively, one can employ Whole Genome Shotgun (WGS) sequence characterization of microbes or a microbial community.

Interactions Between Microbiome and Host

Interactions between the human microbiome and the host shape host health and disease via multiple mechanisms, including the provision of essential functions by the microbiota. Examples of these mechanisms include but are not limited to the function of the microbiota in ensuring a healthy level of bile acid metabolism, energy harvesting and storage, and regulation of immune responses, and reducing deleterious and unhealthy levels of gut permeability or metabolic endotoxemia.

Importance of Bile Acids to Human Health and Role of Microbiota

Primary bile acids, cholic acid (CA) and chenodeoxycholic acid (CDCA) are synthesized from cholesterol in the liver in humans. The synthesized primary bile acids are conjugated to glycine, taurine, or sulfate before secretion into the bile by specific transporters located in the basolateral membrane of the hepatocyte. The ingestion of a meal triggers the release of bile from the gallbladder into the intestinal lumen, where bile acids form micelles with dietary lipids and lipid-soluble vitamins, facilitating their absorption. ˜95% of bile acids are reabsorbed via specific transporters expressed in the distal ileum, and the remaining 5% escapes the enterohepatic cycle and travels towards the large intestine to be excreted in the feces. In the colon, the bile acids may undergo deconjugation and dehydroxylation by the gut microflora. The resulting secondary bile acids are mainly deoxycholic acid (DCA) and lithocholic acid (LCA). The bile acid pool undergoes this enterohepatic cycle around 12×/day in humans. Although the bile acid pool size is constant, the flux of bile acids varies during the day; bile acid flux and plasma bile acid concentrations are highest postprandially (See reviews Prawitt, J et al. 2011 Curr Diab Rep Bile acid metabolism and the pathogenesis of type 2 diabetes 11: 160-166; Nieuwdorp et al. 2014 Gastroenterology. Role of the Microbiome in Energy Regulation and Metabolism. pii: S0016-5085(14)00219-4. doi: 10.1053/j.gastro.2014.02.008).

Commensal bacteria are involved in processing primary bile acids to secondary bile acids in the colon. Known biotransformations of bile acids by commensal GI bacteria include deconjugation of the conjugated bile salts to liberate free bile acids and amino acid moieties, removal of hydroxyl groups principally the C-7 hydroxyl group of the cholic acid moiety, oxidative and reductive reactions of the existing hydroxyl groups, and epimerization of bile acids.

The canonical first step in bile acid metabolism is deconjugation of the taurine or glycine group through enzymes termed bile salt hydrolases, to yield CA and CDCA. These bile acids are then substrates for a series of enzymatic steps that remove the 7-alphahydroxy group to form deoxycholic acid (DCA) and lithocholic acid (LCA). LCA has particularly low solubility due to the loss of hydrophilic side chains compared to any of the other bile acids. It is also feasible for microbes to dehydroxylate the conjugated primary bile acids, giving rise to gluco-DCA; gluco-LCA; tauro-DCA; and tauro-LCA. Further modifications are possible, including the microbial conversion of CDCA to a 7-betahydroxy epimer, ursodeoxycholic acid (UDCA). Many other secondary bile acids are made in smaller amounts by the gut microbiota, for example, alpha-, beta-, gamma-, and omega-muricholic acids and many others (see Swann J R et al., 2011 PNAS Systemic gut microbial modulation of bile acid metabolism in host tissue compartments 108: 4523-30).

Intestinal microbiota play a key role in bile acid metabolism. Germ-free mice have altered metabolism of bile acids, including increased levels of conjugated bile acids throughout the intestine, with no deconjugation, and strongly decreased fecal excretion. Provision of ampicillin to mice increases biliary bile acid output 3-fold and decreases fecal output by 70%.

Dysbiosis of the gut microbiome affecting bile acid metabolism may affect adiposity, glucose regulation, and inflammation, among other effects. Bile acids are essential solubilizers of lipids, fats, and lipid soluble vitamins to enhance absorption of nutrients in the small intestine, and are also signaling molecules that regulate metabolism, including glucose homeostasis and basal metabolic rate. See Houten, S M et al. 2006 EMBO J. Endocrine function of bile acids. 25: 1419-25; Prawitt, J et al. 2011 Curr Diab Rep. Bile acid metabolism and the pathogenesis of type 2 diabetes. 11: 160-166. For example, bile acid sequestrants (non-absorbable polymers that complex bile acids in the intestinal lumen and divert them from the enterohepatic cycle) can improve glycemic control in Type 2 diabetes patients. Prawitt, J et al. 2011 Curr Diab Rep Bile acid metabolism and the pathogenesis of type 2 diabetes 11: 160-166.

The most prominent targets of action by bile acids and their metabolites include FXR (farnesoid X receptor), an orphan nuclear receptor within the liver and intestine, and TGR5, a G-protein coupled receptor found on gallbladder, ileum, colon, brown and white adipose tissue. FXR is preferentially activated by CDCA, and in turn upregulates the expression of gene products including FGF-19 (fibroblast growth factor 19) in humans. FGF-15 (the murine analogue of FGF-19) increases basal metabolic rate and reverses weight gain in mice given a high fat diet. FXR activation also down-regulates hepatic gluconeogenesis. Although both conjugated and unconjugated bile acids can bind to FXR, the conjugated forms must be actively transported into the cell to initiate signaling whereas the unconjugated bile acids can diffuse through the membrane owing to their lower molecular weight, higher pKa and tendency to exist in the protonated form.

TGR5 is preferentially activated by the secondary bile acid LCA and tauro-LCA with downstream effects, among others, on expression of incretin hormones such as GLP-1 that modulate insulin production and help maintain glucose homeostasis.

Bile acids are therefore important metabolic regulators. Additional insight into the importance of the interplay between the gut microbiome, bile acid metabolism, and glucose homeostasis is provided by the observation that treating obese male patients with a 7-day course of vancomycin decreases total microbiota diversity, specifically depleting species in the diverse Clostridium IV and XIVa clusters. Among the Clostridia are various organisms that metabolize bile acids as well as others that produce short chain fatty acids, including butyrate and propionate. In contrast, treatment with a 7-day course of amoxicillin produces a trend toward increased microbiota diversity. Moreover, fecal bile acid composition is markedly changed following vancomycin treatment; secondary bile acids DCA, LCA and iso-LCA decrease whereas primary bile acids CA and CDCA increase. Amoxicillin treatment does not alter the ratio of bile acids in fecal samples. FGF-19 levels in serum are also decreased following vancomycin treatment, but not amoxicillin treatment. Peripheral insulin sensitivity changes following vancomycin but not amoxicillin treatment. Vrieze, A et al., 2013 J Hepatol Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensistivity dx.doi.org/10.1016/j.jhep.2013.11.034.

While the study by Vrieze et al. points out the potential for microbes to improve insulin homeostasis through enhanced secondary bile acid metabolism, the authors point out several limitations of their work. Most importantly, while the HIT-Chip analysis used to generate fecal microbial profiles provides valuable information regarding classes of organisms, it does not provide mechanistic information or identify specific species or functional enzymatic pathways responsible for the observed effects. Moreover, the HIT-Chip is a hybridization based assay and the similarity of sequences among the organisms in the Clostridial clusters may lead to mis-assignments. As a result, others have failed to define specific compositions that can be used to modulate insulin sensitivity via bile acid metabolism.

In addition to the role for bile acids as metabolic regulators, bile acids are also linked to inflammatory disease. Crohn's Disease patients in the Metagenomics of the Human Intestinal Tract (MetaHIT) cohort show reduced bile salt hydrolase (BSH) gene abundance compared to patients without disease, and increased primary bile acids in inflammatory bowel syndrome patients is correlated with stool frequency and consistency (Duboc et al. 2012 Neurogastroenterol Motil. Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome. doi: 10.1111/j.1365-2982.2012.01893.x). Furthermore, TGR5 is expressed on immune monocytes and macrophages in addition to GI and liver tissues, and FXR and TGR5 are known to be involved in regulation of inflammation in enterohepatic tissues (Jones et al., 2014 Expert Opin Biol Ther The human microbiome and bile acid metabolism: dysbiosis, dysmetabolism, disease and intervention doi:10.1517/14712598.2014.880420)

Multiple methods are available for determination of bile acids in serum, bile and faces of individuals. As reviewed by Sharma (Sharma, K R, Review on bile acid analysis, Int J Pharm Biomed Sci 2012, 3(2), 28-34), a variety of methods can be used, such as chemical (Carey J B, et al, 1958, The bile acids in normal human serum with comparative observations in patients with jaundice. J Lab Clin Med 1958, 46, 860-865), thin layer chromatography (Fausa O, and Shalhegg B A. 1976 Quantitative determination of bile acids and their conjugates using thin-layer chromatography and a purified 3-α hydroxysteroid dehydrogenase. Scand J Gastroenterol 9, 249-254.), high performance liquid chromatography (Islam S, et al Fasting serum bile acid level in cirrhosis “A semi quantitative index of hepatic function”. J Hepatol 1985, 1, 609-617; Paauw J D, at al. Assay for taurine conjugates of bile acids in serum by reversed phase high performance liquid chromatography. J Chromatograph B Biomed Appl 1996, 685, 171-175), radioimmunoassay (Wildgrube J, Stockhausan H, Peter M, Mauritz G, Mandawi R. Radioimmunoassay of bile acids in tissues, bile and urine. Clin Chem 1983, 29, 494-498), enzyme linked colorimetric and radioimmunoassay (Guo W, et al. A study on detection of serum fasting total bile acid and chologlycin in neonates for cholestasis. Chin Med Sci J 1996, 11, 244-247.), mass spectrometry (Sjovell J, et al. Mass spectrometry of bile acids. Method in enzymology. Vol. III, Academic Press, New York 1985.), tandem mass spectrometry (Griffiths W J. Tandem mass spectrometry in study of fatty acids, bile acids and steroids. Mass Spectrum Rev 2003, 22, 81-152.), gas chromatography using high resolution glass capillary columns and mass spectrometry (Setchell K D R, Matsui A. Serum bile acid analysis. Clin Chim Acta 1983, 127, 1-17.), gas chromatography (Fischer S, et al. Hepatic levels of bile acids in end stage chronic cholestatic liver disease. Clin Chim Acta 1996, 251, 173-186.), gas liquid chromatography (Van Berge Hengouwen G P et al., Quantitative anaylsis of bile acids in serum and bile, using gas liquid chromatography. Clin Chim Acta 1974, 54, 249-261; Batta A K, et al. Characterization of serum and urinary bile acids in patients with primary biliary cirrhosis by gas-liquid chromatography-mass spectrometry: effect of ursodeoxycholic acid treatment. J Lipid Res 1989, 30, 1953-1962), luminometric method (Styrellius I, Thore A, Bjorkhem I. Luminometric method. In: Methods of enzymatic analysis. (Ed. III). Bergmeyer, Hans Ulirch [Hrsg]. 8: 274-281, 1985.), UV method for bile assay (Stayer E, et al. Fluorimetric method for serum. In: Methods of enzymatic analysis. (Ed.III). Bergmeyer, Hans Ulrich; [Hrsg]. 8, 288-290, 1985; Stayer E, et al. UV method for bile, gastric juice and duodenai aspirates. In: Methods of enzymatic analysis, (e.d.III). Bergmeyer, Hans Ulrich [Hrsg]. 8: 285-287, 1985), enzymatic colorimetric method (Collins B J, et al. Measurement of total bile acids in gastric juice. J Clin Pathol 1984, 37, 313-316) and enzymatic fluorimetric method can be used (Murphy G M, et al. A fluorometric and enzymatic method for the estimation of serum total bile acids. J Clin Path 1970, 23, 594-598; Hanson N Q, Freier E F. Enzymic measurement of total bile acid adapted to the Cobas Fara Centrifugal analyzer. Clin Chem. 1985, 35, 1538-1539).

Importance of Short Chain Fatty Acids (SCFA) to Human Health and Role of Microbiota

Short chain fatty acids (SCFAs) are a principal product of bacterial fermentation in the colon. SCFAs, particularly acetate, propionate and butyrate, are thought to have many potential benefits to the mammalian host. SCFAs are organic acids with fewer than 6 carbons and include acetate, propionate, butyrate, valerate, isovalerate, and 2-methyl butyrate. While longer chain fatty acids are derived primarily from dietary sources, SCFAs are derived from the breakdown of non-digestible plant fiber. Butyrate is a primary energy source for colonocytes, whereas propionate is thought to be metabolized mostly by the liver via portal vein circulation from the colon. Acetate is derived from the microbiota is thought to be more generally available to tissues.

In addition to acting as metabolic substrates, SCFAs have multiple benefits, including that SCFAs produced by the microbiota are essential for immune homeostasis and particularly for immune modulation by regulatory T cells. Direct ingestion of acetate, propionate or butyrate, or a mixture of all three by mice, stimulates the proliferation and maturation of regulatory T cells (Tregs) that reside in the colon. Mice given SCFAs in drinking water have significantly higher levels of colonic CD4+FoxP3+ T cells (Tregs) than germ free and SPFA controls, and these Treg cells are functionally more potent as measured by the expression of IL-10 mRNA and protein, and by their ability to inhibit CD8+ effector T cells in vitro (Smith P M et al. 2013 Science The microbial metabolites, short-chain fatty acid regulate colonic Treg cell homeostasis 341: 569-73). This effect of SCFAs is mediated via signaling through GPR43 (FFAR2), a G protein coupled receptor expressed on a variety of cells but with high frequency on colonic Treg cells. GPR43 signaling is upstream of modification of histone deacetylase activity (particularly HDAC9 and HDCA3), which is known to alter gene expression via reconfiguration of chromatin. Furthermore, the effects of experimental colitis induced by adoptive T cell transfer are reduced by SCFAs including propionate alone and a mixture of acetate, propionate or butyrate in a GPR43 dependent fashion.

Beyond the direct effects of SCFA administered orally to animals, microbes can produce SCFA in situ in the colon and improve outcomes in several disease models. Daily administration of 10⁹ cfu of Butyricicoccus pullicaecorum, a butyrate forming organism first isolated from chickens, for 1 week ameliorates TNBS-induced colitis in a rat model (Eeckhaut V et al., 2013 Gut Progress towards butyrate-producing pharmabiotics: Butyricicoccus pullicaecorum capsule and efficacy in TNBS models in comparison with therapeutics doi:10.1136/gutjnl-2013-305293). In humans, topical administration of butyrate or sodium butyrate via a rectal enema may be beneficial to ulcerative colitis patients (Scheppach W et al. 1992 Gastroenterol Effect of butyrate enemas on the colonic mucosa in distal ulcerative colitis 103: 51-56; Vernia P et al. 2003 Eur. J. Clin. Investig Topical butyrate improves efficacy of 5-ASA in refractory distal ulcerative colitis: results of a multicentre trial. 33: 244-48). Butyrate has effects at multiple levels including signaling via GPR109A, which is expressed on the apical surface of intestinal epithelial cells (IECs). GPR109A lowers NFKB-mediated gene expression, including reduced expression of the inflammatory cytokines TNF-alpha, IL-6 and IL-1beta.

Oral administration of SCFAs in mice also has direct effects on metabolism. SCFAs are a significant energy source and thus fermentation by the microbiota can contribute up 5-10% of the basal energy requirements of a human. SCFAs upregulate production of glucagon-like peptide 1 (GLP-1), peptide (P)YY and insulin. GLP-1 and PYY are noted to play a role in enhancing satiety and reducing food intake. Furthermore, fecal transplantation from lean human donors to obese recipients with metabolic syndrome results in a significant increase in insulin sensitivity after 6 weeks. This change is most correlated with the transfer of Eubacterium hallii, a gram-positive, butyrate-fermenting microbe (Vrieze, A., et al., 2012 Gastroenterol Transfer of intestinal microbiota from lean donors increases insulin sensitivity 143: 913-6).

A common factor underlying both diabetes and obesity is the phenomenon of low-level inflammation termed metabolic endotoxemia (see below). Metabolic endotoxemia refers to increased permeability of the gut (“leaky gut syndrome”) coupled with increased translocation of lipopolysaccharide (LPS), mediating an inflammatory response that triggers insulin resistance, changes in lipid metabolism, and liver inflammation responsible for non-alcoholic fatty liver disease (NAFLD). Low level bacteremia may also lead to the translocation of viable gram-negative organisms into distal tissues, such as adipocytes, and further drive inflammation. SCFAs provide a benefit here as well, both by providing an energy source to enhance colonic epithelial cell integrity and by stimulating the expression of tight junction proteins to reduce translocation of gram-negative LPS, bacterial cells and their fragments (Wang H B et al, 2012 Dig Dis Sci Butyrate enhances intestinal epithelial barrier function via up-regulation of tight junction protein Claudin-1 transcription 57: 3126-35).

For all of these reasons, it would be useful to have microbial communities with an enhanced ability to produce SCFAs for the treatment of diseases such as diabetes, obesity, inflammation, ulcerative colitis and NAFLD.

Acetate, propionate and butyrate are formed as end-products in anaerobic fermentation. SCFA producing bacteria in the gut gain energy by substrate-level phosphorylation during oxidative breakdown of carbon precursors. However, the resulting reducing equivalents, captured in the form of NADH, must be removed to maintain redox balance, and hence the energetic driving force to produce large amounts of reduced end-products such as butyrate and propionate, in order to regenerates NAD+. Acetate, propionate and butyrate are not the only end products of fermentation: microbes in the gut also produce lactate, formate, hydrogen and carbon dioxide depending on the conditions. As discussed below, lactate and acetate can also drive the formation of butyrate and propionate through cross-feeding by one microorganism to another.

The rate of SCFA production in the colon is highly dependent on many factors including the availability of polysaccharide carbon sources (such as, but not limited to, fructans, starches, cellulose, galactomannans, xylans, arabinoxylans, pectins, inulin, fructooligosaccharides, and the like), the presence of alternative electron sinks such as sulfate and nitrate, the redox potential, hydrogen (H₂) partial pressure and pH. As described above, cross-feeding among organisms can also play a role, for instance when a lactate forming organism provides lactate as a substrate for a butyrate or propionate producer, or when a saccharolytic organism breaks down a complex carbohydrate to provide a mono- or disaccharide for fermentation. Acetate, which can be as high as 30 mM in the gut, is also a key building block of butyrate through the action of the enzyme butyryl-CoA:acetate CoA transferase, the final step in the production of butyrate. Importantly, this enzyme can also function as a propionyl-CoA: acetate CoA transferase, resulting in the production of propionate.

Since diet is a principal determinant of the variety of carbon sources and other nutrients available in the colon, it is clear that a functional ecology for SCFA production will comprise multiple organisms capable of adapting to diet-driven changes in in the gut environment. Thus, there exists a need for a bacterial composition that can ferment sufficient quantities of SCFA products in spite of the varying environmental conditions imposed by a changing diet. Such bacterial compositions will comprise organisms capable of fermenting a variety of carbon sources into SCFA.

Role of Microbiota in Metabolic Endotoxemia/Bacteremia

Chronic, low-grade inflammation is characteristic of obesity and is recognized to play an underlying pathogenic role in the metabolic complications and negative health outcomes of the disease. Notably, obesity is associated with elevated plasma levels of bacterial lipopolysaccharide (LPS). Energy intake, in particular a high fat diet (HFD), increases gut permeability and increases plasma LPS levels 2- to 3-fold. LPS in the circulatory system reflects passage of bacterial fragments across the gut into systemic circulation (termed “metabolic endotoxemia”), either through increases in diffusion due to intestinal paracellular permeability or through absorption by enterocytes during chylomicron secretion. Subcutaneous infusion of LPS into wild type mice maintained on a normal chow diet for 4 weeks leads to increased whole body, liver and adipose tissue weights, adipose and liver inflammation as well as fasted hyperglycemia and insulinemia, effects that are comparable to those induced by HFD (Cani et al., 2007 Diabetes. Metabolic endotoxemia initiates obesity and insulin resistance doi:10.2337/db06-1491). In addition to bacterial fragments, the translocation of live bacteria to host tissues may also be a feature of obesity (termed “metabolic bacteremia”) (Shen et al., 2013 Mol Aspects Med. The gut microbiota, obesity and insulin resistance doi: 10.1016/j.mam.2012.11.001).

Host-microbiota interactions at the gut mucosal interface are involved in intestinal barrier functionality and bacterial surveillance/detection. Dysbiosis can promote bacterial translocation and obesity-associated inflammation. In one instance, metabolic endotoxemia of HFD-induced obesity in mice is associated with reductions in Bifidobacterium, and both may be ameliorated through treatment with inulin (oligofructose) (Cani et al. Diabetologia Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia doi: 10.1007/s00125-007-0791-0). The beneficial effects of inulin and Bifidobacterium are associated with enhanced production of intestinotrophic proglucagon-derived peptide 2 (GLP-2), a peptide produced by L cells of the intestine that promotes intestinal growth (Cani et al. Gut. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. doi: 10.1136/gut.2008.165886). Alternative pathways involving host-microbiota interactions and intestinal barrier integrity and metabolic endotoxemia/bacteremia include but are not limited to those involving intestinotrophic proglucagon-derived peptide (GLP)-2, endocannabinoid (eCB) signaling, and pattern recognition receptors including nucleotide-binding oligomerization domain (NOD)-like receptors (NLR) such as NOD1/NLRC1 and NOD2/NLRC2 as well as Toll like receptors (TLR) such as TLR-2, TLR-4, TLR-5 and TLR adapter protein myeloid differentiation primary-response protein 88 (MyD88) (see review Shen et al., 2013 Mol Aspects Med. The gut microbiota, obesity and insulin resistance doi: 10.1016/j.mam.2012.11.001).

Role of Microbiota in Energy Harvesting and Storage

The gut microbiota is involved in host energy harvesting. Germ free (GF) mice consume more energy but are significantly leaner than wild type counterparts. Conventionalization of GF mice given a low-fat, polysaccharide-rich diet with the microbiota of conventionally-raised mice leads to 60% more adiposity and insulin resistance despite reduced food intake (Backhed et al., 2004 PNAS The gut microbiota as an environmental factor that regulates fat storage doi: 10.1073/pnas.0407076101). GF mice conventionalized with microbiota from obese mice show significantly greater increase in total body fat than GF mice conventionalized with microbiota from lean mice. Obese (ob/ob) mice have significantly less energy remaining in their feces relative to their lean littermates as measured by bomb calorimetry (Turnbaugh et al. 2006 Nature. An obesity-associated gut microbiome with increased capacity for energy harvest doi: 10.1038/nature05414). In humans, “overnutrition” (defined as energy consumption as a percentage of weight-maintaining energy needs) is associated with proportionally more Firmicutes and fewer Bacteroidetes and energy loss (stool calories as a percentage of ingested calories) in lean subjects is negatively associated with the proportional change in Firmicutes and positively associated with the proportional change in Bacteroidetes, suggesting impact of the gut microbiota on host energy harvest (Jumpertz et al., 2011 Am J Clin Nutr. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. doi: 10.3945/ajcn.110.010132).

In addition to affecting host energy harvesting, gut microbiota is also implicated in energy storage. The increase in body fat observed upon conventionalization of GF mice is associated with a decrease in Fasting-induced adipose factor (Fiaf) expression in the ileum and a 122% increase in Lipoprotein Lipase (LPL) activity in epididymal adipose tissue (Backhed et al., 2004 PNAS The gut microbiota as an environmental factor that regulates fat storage doi/10.1073/pnas.0407076101). Fiaf (also known as angiopoietin-like 4) is a protein secreted by adipose tissues, liver and intestine that inhibits the activity of LPL, a key enzyme in the hydrolysis of lipoprotein-associated triglycerides and the release of fatty acids for transport into cells. In adipocytes, fatty acids released by LPL are re-esterified into triglyceride and stored as fat (Shen et al., 2013 Mol Aspects Med. The gut microbiota, obesity and insulin resistance doi: 10.1016/j.mam.2012.11.001).

Other Functional Pathways

The pathways and mechanisms discussed above on the functional pathways and mechanisms by which the microbiota shape host health and disease is not meant to be exhaustive. Alternative functional pathways and mechanisms exist, including but not limited to pathways involving AMP-activated protein kinase (AMPK), TLR-5, and SREBP-1c and ChREBP.

Emergence of Antibiotic Resistance in Bacteria

Antibiotic resistance is an emerging public health issue (Carlet J, Collignon P, Goldmann D, Goossens H, Gyssens I C, Harbarth S, Jarlier V, Levy S B, N′Doye B, Pittet D, et al. 2011. Society's failure to protect a precious resource: antibiotics. Lancet 378: 369-371.). Numerous genera of bacteria harbor species that are developing resistance to antibiotics. These include but are not limited to Vancomycin Resistant Enterococcus (VRE) and Carbapenem resistant Klebsiella (CRKp). Klebsiella pneumoniae and Escherichia coli strains are becoming resistant to carbapenems and require the use of old antibiotics characterized by high toxicity, such as colistin (Canton R, Akóva M, Carmeli Y, Giske C G, Glupczynski Y, Gniadkowski M, Livermore D M, Miriagou V, Naas T, Rossolini G M, et al. 2012. Rapid evolution and spread of carbapenemases among Enterobacteriaceae in Europe. Clin Microbiol Infect 18: 413-431.). Further multiply drug resistant strains of multiple species, including Pseudomonas aeruginosa, Enterobacter spp, and Acinetobacter spp are observed clinically including isolates that are highly resistant to ceftazidime, carbapenems, and quinolones (European Centre for Disease Prevention and Control: EARSS net database. ecdc.europa.eu). The Centers for Disease Control and Prevention in 2013 released a Threat Report (cdc.gov/drugresistance/threat_report 2013) citing numerous bacterial infection threats that included Clostridium difficile, Carbapenem-resistant Enterobacteriaceae (CRE), Multidrug-resistant Acinetobacter, Drug-resistant Campylobacter, Extended spectrum β-lactamase producing Enterobacteriaceae (ESBLs), Vancomycin-resistant Enterococcus (VRE), Multidrug-resistant Pseudomonas aeruginosa, Drug-resistant Non-typhoidal Salmonella, Drug-resistant Salmonella Typhi, Drug-resistant Shigella, Methicillin-resistant Staphylococcus aureus (MRSA), Drug-resistant Streptococcus pneumoniae, Vancomycin-resistant Staphylococcus aureus (VRSA), Erythromycin-resistant Group A Streptococcus, and Clindamycin-resistant Group B Streptococcus. The increasing failure of antibiotics due the rise of resistant microbes demands new therapeutics to treat bacterial infections. Administration of a microbiome therapeutic bacterial composition offers potential for such therapies. Applicants have discovered that patients suffering from recurrent C. difficile associated diarrhea (CDAD) often harbor antibiotic resistant Gram-negative bacteria, in particular Enterobacteriaceae and that treatment with a bacterial composition effectively treats CDAD and reduces the antibiotic resistant Gram-negative bacteria. The gastrointestinal tract is implicated as a reservoir for many of these organisms including VRE, MRSA, Pseudomonas aeruginosa, Acinetobacter and the yeast Candida (Donskey, Clinical Infectious Diseases 2004 39:214,The Role of the Intestinal Tract as a Reservoir and Source for Transmission of Nosocomial Pathogens), and thus as a source of nosocomial infections. Antibiotic treatment and other decontamination procedures are among the tools in use to reduce colonization of these organisms in susceptible patients including those who are immunosuppressed. Bacterial-based therapeutics would provide a new tool for decolonization, with a key benefit of not promoting antibiotic resistance as antibiotic therapies do.

Compositions of the Invention

Network Ecologies

As described above, the Network Ecology and Functional Network Ecology refer to a consortium of OTUs or Functional modalities respectively that co-occur in a group of subjects. The network is defined mathematically by a graph delineating how specific nodes (i.e., OTUs or functional modalities) and edges (connections between specific OTUs or functional modalities) relate to one another to define the structural ecology of a consortium of OTUs or functions. Any given Network Ecology or Functional Network Ecology will possess inherent phylogenetic diversity and functional properties.

A Network Class or Core Network refers to a group of Network Ecologies or Functional Network ecologies that are computationally determined to comprise ecologies with similar phylogenetic and/or functional characteristics. A Network Class or Core Network therefore contains important biological features, defined either phylogenetically or functionally, of a group (i.e., a cluster) of related network ecologies.

Keystone OTUs or Functions are one or more OTUs or Functions that are common to many network Ecologies or Functional Netwok Ecologies and are members of Networks Ecologies or Functional Network Ecologies that occur in many subjects (i.e., are pervasive). Due to the ubiquitous nature of Keystone OTUs and Functions, they are central to the function of network ecologies in healthy subjects and are often missing or at reduced levels in subjects with disease. Keystone OTUs and Functions may exist in low, moderate, or high abundance in subjects.

Bacteria that are members of the keystone OTUs, core network or network ecology are provided herein.

Bacterial Compositions

Provided are bacteria and combinations of bacteria that comprise network ecologies and functional network ecologies of the human gut microbiota. The bacteria and combinations of bacteria that comprise network ecologies have a capacity to meaningfully provide functions of a healthy microbiota when administered to mammalian hosts. Without being limited to a specific mechanism, it is believed that the members of network ecologies can inhibit the growth, proliferation, germination and/or colonization of one or a plurality of pathogenic bacteria in the dysbiotic microbiotal niche, and may also augment the growth, proliferation, germination and/or colonization of desired bacteria so that a healthy, diverse and protective microbiota colonizes and populates the intestinal lumen to establish or reestablish ecological control over pathogens or potential pathogens (e.g., some bacteria are pathogenic bacteria only when present in a dysbiotic environment). The term pathogens refers to a bacterium or a group of bacteria or any other organism or entity that is capable of causing or affecting a disease, disorder or condition of a host containing the bacterium, organism or entity, including but not limited to metabolic diseases such as prediabetes, type 1 diabetes, and type 2 diabetes.

As used herein, a “type” or more than one “types” of bacteria may be differentiated at the genus level, the species, level, the sub-species level, the strain level or by any other taxonomic method, as described herein and otherwise known in the art.

Bacterial compositions can comprise two types of bacteria (termed “binary combinations” or “binary pairs”), and typically a large number of bacteria types. For instance, a bacterial composition can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21, 22, 23, 24, 25, 26, 27, 28, 29 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or at least 40, at least 50 or greater than 50 types of bacteria, as defined by species or operational taxonomic unit (OTU), or otherwise as provided herein. In some embodiments, the bacterial composition includes at least 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, or greater numbers of bacteria types.

In another embodiment, the number of types of bacteria present in a bacterial composition is at or below a known value. For example, in such embodiments the network ecology comprises 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50 or fewer types of bacteria, such as 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, or 10 or fewer, or 9 or fewer types of bacteria, 8 or fewer types of bacteria, 7 or fewer types of bacteria, 6 or fewer types of bacteria, 5 or fewer types of bacteria, 4 or fewer types of bacteria, or 3 or fewer types of bacteria.

Bacterial Compositions Described by Species

Bacterial compositions that comprise network ecologies may be prepared comprising at least two types of isolated bacteria, chosen from the species in Table 1.

In one embodiment, the bacterial composition that comprises at least one and preferably more than one of the following: Enterococcus faecalis (previously known as Streptococcus faecalis), Clostridium innocuum, Clostridium ramosum, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaoiotaomicron, Escherichia coli (1109 and 1108-1), Clostridum bifermentans, and Blautia producta (previously known as Peptostreptococcus productus). In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition comprises at least one and preferably more than one of the following: Enterococcus faecalis (previously known as Streptococcus faecalis), Clostridium innocuum, Clostridium ramosum, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaoiotaomicron, Escherichia coli (1109 and 1108-1), Clostridum bifermentans, and Blautia producta (previously known as Peptostreptococcus productus). In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In another embodiment, the bacterial composition comprises at least one and preferably more than one of the following: Acidaminococcus intestinalis, Bacteroides ovatus, two strains of Bifidobacterium adolescentis, two strains of Bifidobacterium longum, Blautia producta, Clostridium cocleatum, Collinsella aerofaciens, two strains of Dorea longicatena, Escherichia coli, Eubacterium desmolans, Eubacterium eligens, Eubacterium limosum, four strains of Eubacterium rectale, Eubacterium ventriosumi, Faecalibacterium prausnitzii, Lachnospira pectinoshiza, Lactobacillus casei, Lactobacillus casei/paracasei, Paracateroides distasonis, Raoultella sp., one strain of Roseburia (chosen from Roseburia faecalis or Roseburia faecis), Roseburia intestinalis, two strains of Ruminococcus torques, two strains of Ruminococcus obeum, and Streptococcus mitis. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In yet another embodiment, the bacterial composition comprises at least one and preferably more than one of the following: Barnesiella intestinihominis; Lactobacillus reuteri; a species characterized as one of Enterococcus hirae, Enterococus faecium, or Enterococcus durans; a species characterized as one of Anaerostipes caccae or Clostridium indolis; a species characterized as one of Staphylococcus warneri or Staphylococcus pasteuri; and Adlercreutzia equolifaciens. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In other embodiments, the bacterial composition comprises at least one and preferably more than one of the following: Clostridium absonum, Clostridium argentinense, Clostridium baratii, Clostridium bartlettii, Clostridium bifermentans, Clostridium botulinum, Clostridium butyricum, Clostridium cadaveris, Clostridium camis, Clostridium celatum, Clostridium chauvoei, Clostridium clostridioforme, Clostridium cochlearium, Clostridium difficile, Clostridium fallax, Clostridium felsineum, Clostridium ghonii, Clostridium glycolicum, Clostridium haemolyticum, Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis, Clostridium innocuum, Clostridium irregulare, Clostridium limosum, Clostridium malenominatum, Clostridium novyi, Clostridium oroticum, Clostridium paraputrificum, Clostridium perfringens, Clostridium piliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridium ramosum, Clostridium sardiniense, Clostridium sartagoforme, Clostridium scindens, Clostridium septicum, Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridium subterminale, Clostridium symbiosum, Clostridium tertium, Clostridium tetani, Clostridium welchii, and Clostridium villosum. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Clostridium innocuum, Clostridum bifermentans, Clostridium butyricum, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis, three strains of Escherichia coli, and Lactobacillus sp. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Clostridium bifermentans, Clostridium innocuum, Clostridium butyricum, three strains of Escherichia coli, three strains of Bacteroides, and Blautia producta. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Bacteroides sp., Escherichia coli, and non pathogenic Clostridia, including Clostridium innocuum, Clostridium bifermentans and Clostridium ramosum. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Bacteroides species, Escherichia coli and non-pathogenic Clostridia, such as Clostridium butyricum, Clostridium bifermentans and Clostridium innocuum. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Bacteroides caccae, Bacteroides capillosus, Bacteroides coagulans, Bacteroides distasonis, Bacteroides eggerthii, Bacteroides forsythus, Bacteroides fragilis, Bacteroides fragilis-ryhm, Bacteroides gracilis, Bacteroides levii, Bacteroides macacae, Bacteroides merdae, Bacteroides ovatus, Bacteroides pneumosintes, Bacteroides putredinis, Bacteroides pyogenes, Bacteroides splanchnicus, Bacteroides stercoris, Bacteroides tectum, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides ureolyticus, and Bacteroides vulgatus. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Bacteroides, Eubacteria, Fusobacteria, Propionibacteria, Lactobacilli, anaerobic cocci, Ruminococcus, Escherichia coli, Gemmiger, Desulfomonas, and Peptostreptococcus. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

In one embodiment, the bacterial composition that comprises a network ecology comprises at least one and preferably more than one of the following: Bacteroides fragilis ss. Vulgatus, Eubacterium aerofaciens, Bacteroides fragilis ss. Thetaiotaomicron, Blautia producta (previously known as Peptostreptococcus productus II), Bacteroides fragilis ss. Distasonis, Fusobacterium prausnitzii, Coprococcus eutactus, Eubacterium aerofaciens III, Blautia producta (previously known as Peptostreptococcus productus I), Ruminococcus bronii, Bifidobacterium adolescentis, Gemmiger formicilis, Bifidobacterium longum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectale Eubacterium rectale IV, Eubacterium eligens, Bacteroides eggerthii, Clostridium leptum, Bacteroides fragilis ss. A, Eubacterium biforme, Bifidobacterium infantis, Eubacterium rectale III-F, Coprococcus comes, Bacteroides capillosus, Ruminococcus albus, Eubacterium formicigenerans, Eubacterium hallii, Eubacterium ventriosum I, Fusobacterium russii, Ruminococcus obeum, Eubacterium rectale II, Clostridium ramosum I, Lactobacillus leichmanii, Ruminococcus cailidus, Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacterium ventriosum, Bacteroides fragilis ss. fragilis, Bacteroides AR, Coprococcus catus, Eubacterium hadrum, Eubacterium cylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis, Peptostreptococcus BL, Eubacterium limosum, Bacteroides praeacutus, Bacteroides L, Fusobacterium mortiferum Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1, Eubacterium AG, -AK, -AL, -AL-1, -AN; Bacteroides fragilis ss. ovatus, -ss. d, -ss. f; Bacteroides L-1, L-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichia coli, Streptococcus morbiliorum, Peptococcus magnus, Peptococcus G, AU-2; Streptococcus intermedius, Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, —CC; Eubacterium tenue, Eubacterium ramulus, Eubacterium AE, -AG-H, -AG-M, AJ, -BN-1; Bacteroides clostridiiformis ss. clostridliformis, Bacteroides coagulans, Bacteroides orails, Bacteroides ruminicola ss. brevis, -ss. ruminicola, Bacteroides splanchnicus, Desuifomonas pigra, Bacteroides L-4, -N-i; Fusobacterium H, Lactobacillus G, and Succinivibrio A. In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition.

Bacterial Compositions Described by Operational Taxonomic Unit (OTUs)

Bacterial compositions may be prepared comprising at least two types of isolated bacteria, chosen from the SEQ ID Numbers (OTUs) in Table 1.

OTUs can be defined either by full 16S sequencing of the rRNA gene (Table 1), by sequencing of a specific hypervariable region of this gene (i.e. V1, V2, V3, V4, V5, V6, V7, V8, or V9), or by sequencing of any combination of hypervariable regions from this gene (e.g. V1-3 or V3-5). The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most microbes.

Using well known techniques, in order to determine the full 16S sequence or the sequence of any hypervariable region of the 16S sequence, genomic DNA is extracted from a bacterial sample, the 16S rDNA (full region or specific hypervariable regions) amplified using polymerase chain reaction (PCR), the PCR products cleaned, and nucleotide sequences delineated to determine the genetic composition of 16S gene or subdomain of the gene. If full 16S sequencing is performed, the sequencing method used may be, but is not limited to, Sanger sequencing. If one or more hypervariable regions are used, such as the V4 region, the sequencing can be, but is not limited to being, performed using the Sanger method or using a next-generation sequencing method, such as an Illumina (sequencing by synthesis) method using barcoded primers allowing for multiplex reactions.

OTUs can be defined by a combination of nucleotide markers or genes, in particular highly conserved genes (e.g., “house-keeping” genes), or a combination thereof, full-genome sequence, or partial genome sequence generated using amplified genetic products, or whole genome sequence (WGS). Using well defined methods familiar to one with ordinary skill in the art, DNA extracted from a bacterial sample will have specific genomic regions amplified using PCR and sequenced to determine the nucleotide sequence of the amplified products. In the whole genome shotgun (WGS) method, extracted DNA will be directly sequenced without amplification. Sequence data can be generated using any sequencing technology including, but not limited to Sanger, Illumina, 454 Life Sciences, Ion Torrent, ABI, Pacific Biosciences, and/or Oxford Nanopore.

In one embodiment, the OTUs can be characterized by one or more of the variable regions of the 16S sequence (V1-V9). These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. (See, e.g., Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805 (1978)). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU.

Bacterial Compositions Exclusive of Certain Bacterial Species Or Strains

In one embodiment, the bacterial composition does not comprise at least one of Enterococcus faecalis (previously known as Streptococcus faecalis), Clostridium innocuum, Clostridium ramosum, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaoiotaomicron, Escherichia coli (1109 and 1108-1), Clostridum bifermentans, and Blautia producta (previously known as Peptostreptococcus productus).

In another embodiment, the bacterial composition does not comprise at least one of Acidaminococcus intestinalis, Bacteroides ovatus, two species of Bifidobacterium adolescentis, two species of Bifidobacterium longum, Collinsella aerofaciens, two species of Dorea longicatena, Escherichia coli, Eubacterium eligens, Eubacterium limosum, four species of Eubacterium rectale, Eubacterium ventriosumi, Faecalibacterium prausnitzii, Lactobacillus casei, Lactobacillus paracasei, Paracateroides distasonis, Raoultella sp., one species of Roseburia (chosen from Roseburia faecalis or Roseburia faecis), Roseburia intestinalis, two species of Ruminococcus torques, and Streptococcus mitis.

In yet another embodiment, the bacterial composition does not comprise at least one of Barnesiella intestinihominis; Lactobacillus reuteri; a species characterized as one of Enterococcus hirae, Enterococus faecium, or Enterococcus durans; a species characterized as one of Anaerostipes caccae or Clostridium indolis; a species characterized as one of Staphylococcus warneri or Staphylococcus pasteuri; and Adlercreutzia equolifaciens.

In other embodiments, the bacterial composition does not comprise at least one of Clostridium absonum, Clostridium argentinense, Clostridium baratii, Clostridium bifermentans, Clostridium botulinum, Clostridium butyricum, Clostridium cadaveris, Clostridium camis, Clostridium celatum, Clostridium chauvoei, Clostridium clostridioforme, Clostridium cochlearium, Clostridium difficile, Clostridium fallax, Clostridium felsineum, Clostridium ghonii, Clostridium glycolicum, Clostridium haemolyticum, Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis, Clostridium innocuum, Clostridium irregulare, Clostridium limosum, Clostridium malenominatum, Clostridium novyi, Clostridium oroticum, Clostridium paraputrificum, Clostridium perfringens, Clostridium piliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridium ramosum, Clostridium sardiniense, Clostridium sartagoforme, Clostridium scindens, Clostridium septicum, Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridium subterminale, Clostridium symbiosum, Clostridium tertium, Clostridium tetani, Clostridium welchii, and Clostridium villosum.

In another embodiment, the bacterial composition does not comprise at least one of Clostridium innocuum, Clostridum bifermentans, Clostridium butyricum, Bacteroides Bacteroides thetaiotaomicron, Bacteroides uniformis, three strains of Escherichia coli, and Lactobacillus sp.

In another embodiment, the bacterial composition does not comprise at least one of Clostridium bifermentans, Clostridium innocuum, Clostridium butyricum, three strains of Escherichia coli, three strains of Bacteroides, and Blautia producta (previously known as Peptostreptococcus productus).

In another embodiment, the bacterial composition does not comprise at least one of Bacteroides sp., Escherichia coli, and non pathogenic Clostridia, including Clostridium innocuum, Clostridium bifermentans and Clostridium ramosum.

In another embodiment, the bacterial composition does not comprise at least one of more than one Bacteroides species, Escherichia coli and non-pathogenic Clostridia, such as Clostridium butyricum, Clostridium bifermentans and Clostridium innocuum.

In another embodiment, the bacterial composition does not comprise at least one of Bacteroides caccae, Bacteroides capillosus, Bacteroides coagulans, Bacteroides distasonis, Bacteroides eggerthii, Bacteroides forsythus, Bacteroides fragilis, Bacteroides fragilis-ryhm, Bacteroides gracilis, Bacteroides levii, Bacteroides macacae, Bacteroides merdae, Bacteroides ovatus, Bacteroides pneumosintes, Bacteroides putredinis, Bacteroides pyogenes, Bacteroides splanchnicus, Bacteroides stercoris, Bacteroides tectum, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides ureolyticus, and Bacteroides vulgatus.

In another embodiment, the bacterial composition does not comprise at least one of Bacteroides, Eubacteria, Fusobacteria, Propionibacteria, Lactobacilli, anaerobic cocci, Ruminococcus, Escherichia coli, Gemmiger, Desulfomonas, and Peptostreptococcus.

In another embodiment, the bacterial composition does not comprise at least one of Bacteroides fragilis ss. Vulgatus, Eubacterium aerofaciens, Bacteroides fragilis ss. Thetaiotaomicron, Blautia producta (previously known as Peptostreptococcus productus II), Bacteroides fragilis ss. Distasonis, Fusobacterium prausnitzii, Coprococcus eutactus, Eubacterium aerofaciens III, Blautia producta (previously known as Peptostreptococcus productus I), Ruminococcus bromii, Bifidobacterium adolescentis, Gemmiger formicilis, Bifidobacterium longum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectale III-H, Eubacterium rectale IV Eubacterium eligens, Bacteroides eggerthii, Clostridium leptum, Bacteroides fragilis ss. A, Eubacterium biforme, Bifidobacterium infantis, Eubacterium rectale III-F; Coprococcus comes, Bacteroides capillosus, Ruminococcus albus, Eubacterium formicigenerans, Eubacterium hallii, Eubacterium ventriosum I, Fusobacterium russii, Ruminococcus obeum, Eubacterium rectale II, Clostridium ramosum I, Lactobacillus leichmanii, Ruminococcus cailidus, Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacterium ventriosum, Bacteroides fragilis ss. fragilis, Bacteroides AR, Coprococcus catus, Eubacterium hadrum, Eubacterium cylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis, Peptostreptococcus BL, Eubacterium limosum, Bacteroides praeacutus, Bacteroides L, Fusobacterium mortiferum I, Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1, Eubacterium AG, -AK, -AL, -AL-1, AN; Bacteroides fragilis ss. ovatus, -ss. d, -ss. f; Bacteroides L-1, L-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichia coli, Streptococcus morbiliorum, Peptococcus magnus, Peptococcus G, AU-2; Streptococcus intermedius, Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, —CC; Eubacterium tenue, Eubacterium ramulus, Eubacterium AE, -AG-H, -AG-M, AJ, -BN-1; Bacteroides clostridiiformis ss. clostridliformis, Bacteroides coagulans, Bacteroides orails, Bacteroides ruminicola ss. brevis, -ss. ruminicola, Bacteroides splanchnicus, Desuifomonas pigra, Bacteroides L-4, -N-i; Fusobacterium H, Lactobacillus G, and Succinivibrio A.

Inhibition of Bacterial Pathogens

In some embodiments, the bacterial composition provides a protective or therapeutic effect against infection by one or more GI pathogens of interest. Table 1 provides a list of OTUs that are either pathogens, pathobionts, or opportunistic pathogens.

In some embodiments, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, extended spectrum beta-lactam resistant Enterococci (ESBL), Carbapenem-resistent Enterobacteriaceae (CRE), and vancomycin-resistant Enterococci (VRE).

In some embodiments, these pathogens include, but are not limited to, Aeromonas hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium difficile, Clostridium perfringens, enteroaggregative Escherichia coli, enterohemorrhagic Escherichia coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia coli (such as, but not limited to, LT and/or ST), Escherichia coli 0157:H7, Helicobacter pylori, Klebsiellia pneumonia, Lysteria monocytogenes, Plesiomonas shigelloides, Salmonella spp., Salmonella typhi, Salmonella paratyphi, Shigella spp., Staphylococcus spp., Staphylococcus aureus, vancomycin-resistant enterococcus spp., Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica.

In one embodiment, the pathogen of interest is at least one pathogen chosen from Clostridium difficile, Salmonella spp., pathogenic Escherichia coli, vancomycin-resistant Enterococcus spp., and extended spectrum beta-lactam resistant Enterococci (ESBL).

Purified Spore Populations

In some embodiments, the bacterial compositions comprise purified spore populations or a combination of a purified spore population with a non-spore population. Purified spore populations contain combinations of commensal bacteria of the human gut microbiota with the capacity to meaningfully provide functions of a healthy microbiota when administered to a mammalian subject. Without being limited to a specific mechanism, it is thought that such compositions inhibit the growth of a pathogen such as C. difficile, Salmonella spp., enteropathogenic E. coli, and vancomycin-resistant Enterococcus spp., so that a healthy, diverse and protective microbiota can be maintained or, in the case of pathogenic bacterial infections such as C. difficile infection, repopulate the intestinal lumen to reestablish ecological control over potential pathogens. In some embodiments, yeast spores and other fungal spores are also purified and selected for therapeutic use.

Disclosed herein are therapeutic and prophylactic compositions containing non-pathogenic, germination-competent bacterial spores, spore forming organisms and non-spore forming organisms, for the prevention, control, and treatment of gastrointestinal diseases, disorders and conditions and for general nutritional health. These compositions are advantageous in being suitable for safe administration to humans and other mammalian subjects and are efficacious in numerous gastrointestinal diseases, disorders and conditions and in general nutritional health. While spore-based compositions are known, these are generally prepared according to various techniques such as lyophilization or spray-drying of liquid bacterial cultures, resulting in poor efficacy, instability, substantial variability and lack of adequate safety.

It has now been found that populations of bacterial spores can be obtained from biological materials obtained from mammalian subjects, including humans. These populations are formulated into compositions as provided herein, and administered to mammalian subjects using the methods as provided herein.

Provided herein are therapeutic bacterial compositions containing a purified population of bacterial spores, spore forming organisms and non-spore forming organisms.

As used herein, the terms “purify”, “purified” and “purifying” refer to the state of a population (e.g., a plurality of known or unknown amount and/or concentration) of desired bacterial spores or bacteria, that have undergone one or more processes of purification, e.g., a selection or an enrichment of the desired bacterial spore, or alternatively a removal or reduction of residual habitat products as described herein. In some embodiments, a purified population has no detectable undesired activity or, alternatively, the level or amount of the undesired activity is at or below an acceptable level or amount. In other embodiments, a purified population has an amount and/or concentration of desired bacterial spores or bacteria at or above an acceptable amount and/or concentration. In other embodiments, the purified population of bacterial spores or bacteria is enriched as compared to the starting material (e.g., a fecal material liquid culture) from which the population is obtained. This enrichment may be by 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, 99.999%, 99.9999%, or greater than 99.9999% as compared to the starting material.

In certain embodiments, the purified populations of bacterial spores have reduced or undetectable levels of one or more pathogenic activities, such as toxicity, an infection of the mammalian recipient subject, an immunomodulatory activity, an autoimmune response, a metabolic response, or an inflammatory response or a neurological response. Such a reduction in a pathogenic activity may be by 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, 99.999%, 99.9999%, or greater than 99.9999% as compared to the starting material. In other embodiments, the purified populations of bacterial spores have reduced sensory components as compared to fecal material, such as reduced odor, taste, appearance, and umami.

Provided are purified populations of bacterial spores or bacteria that are substantially free of residual habitat products. In certain embodiments, this means that the bacterial spore or bacterial composition no longer contains a substantial amount of the biological matter associated with the microbial community while living on or in the human or animal subject, and the purified population of spores may be 100% free, 99% free, 98% free, 97% free, 96% free, or 95% free of any contamination of the biological matter associated with the microbial community. Substantially free of residual habitat products may also mean that the bacterial spore composition contains no detectable cells from a human or animal, and that only microbial cells are detectable, in particular, only desired microbial cells are detectable. In another embodiment, it means that fewer than 1×10′%, 1×10⁻³%, 1×10⁻⁴%, 1×10⁻⁵%, 1×10⁻⁶%, 1×10⁻⁷%, 1×10⁻⁸% of the cells in the bacterial composition are human or animal, as compared to microbial cells. In another embodiment, the residual habitat product present in the purified population is reduced at least a certain level from the fecal material obtained from the mammalian donor subject, e.g., reduced by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, 99.999%, 99.9999%, or greater than 99.9999%.

In one embodiment, substantially free of residual habitat products or substantially free of a detectable level of a pathogenic material means that the bacterial composition contains no detectable viral (including bacterial viruses (i.e., phage)), fungal, or mycoplasmal or toxoplasmal contaminants, or a eukaryotic parasite such as a helminth. Alternatively, the purified spore populations are substantially free of an acellular material, e.g., DNA, viral coat material, or non-viable bacterial material.

As described herein, purified spore populations can be demonstrated by genetic analysis (e.g., PCR, DNA sequencing), serology and antigen analysis, and methods using instrumentation such as flow cytometry with reagents that distinguish desired bacterial spores from non-desired, contaminating materials.

Exemplary biological materials include fecal materials such as feces or materials isolated from the various segments of the small and large intestines. Fecal materials are obtained from a mammalian donor subject, or can be obtained from more than one donor subject, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 200, 300, 400, 500, 750, 1000 or from greater than 1000 donors, where such materials are then pooled prior to purification of the desired bacterial spores.

In alternative embodiments, the desired bacterial spores or bacteria are purified from a single fecal material sample obtained from a single donor, and after such purification are combined with purified spore populations or bacteria from other purifications, either from the same donor at a different time, or from one or more different donors, or both.

Preferred bacterial genera include Acetonema, Alkaliphilus, Alicyclobacillus, Amphibacillus, Ammonifex, Anaerobacter, Anaerofustis, Anaerostipes, Anaerotruncus, Anoxybacillus, Bacillus, Blautia, Brevibacillus, Bryantella, Caldicellulosiruptor, Caloramator, Candidatus, Carboxydibrachium, Carboxydothermus, Clostridium, Cohnella, Coprococcus, Dendrosporobacter Desulfitobacterium, Desulfosporosinus, Desulfotomaculum, Dorea, Eubacterium, Faecalibacterium, Filifactor, Geobacillus, Halobacteroides, Heliobacillus, Heliobacterium, Heliophilum, Heliorestis, Lachnoanaerobaculum, Lysinibacillus, Moorella, Oceanobacillus, Orenia (S.), Oxalophagus, Oxobacter, Paenibacillus, Pelospora, Pelotomaculum, Propionispora, Roseburia, Ruminococcus, Sarcina, Sporobacterium, Sporohalobacter, Sporolactobacillus, Sporomusa, Sporosarcina, Sporotomaculum, Subdoligranulum, Symbiobacterium, Syntrophobotulus, Syntrophospora, Terribacillus, Thermoanaerobacter, and Thermosinus.

In some embodiments, spore-forming bacteria are identified by the presence of nucleic acid sequences that modulate sporulation. In particular, signature sporulation genes are highly conserved across members of distantly related genera including Clostridium and Bacillus. Traditional approaches of forward genetics have identified many, if not all, genes that are essential for sporulation (spo). The developmental program of sporulation is governed in part by the successive action of four compartment-specific sigma factors (appearing in the order σF, σE, σG and σK), whose activities are confined to the forespore (σF and σG) or the mother cell (σE and σK).

Provided are spore populations containing more than one type of bacterium. As used herein, a “type” or more than one “types” of bacteria may be differentiated at the genus level, the species, level, the sub-species level, the strain level or by any other taxonomic method, as described herein and otherwise known in the art.

In some embodiments, all or essentially all of the bacterial spores or bacterial species present in a purified population are originally isolated obtained from a fecal material treated as described herein or otherwise known in the art. In alternative embodiments, one or more than one bacterial spores, bacteria, or types of bacterial spores are generated in culture and combined to form a purified bacterial composition, including a purified spore population. In other alternative embodiments, one or more of these culture-generated populations are combined with a fecal material-derived populations to generate a hybrid population. Bacterial compositions may contain at least two types of these preferred bacteria, including strains of the same species. For instance, a bacterial composition may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 or more than 20 types of bacteria, as defined by species or operational taxonomic unit (OTU) encompassing such species.

Thus, provided herein are methods for production of a bacterial composition containing a population of bacterial spores suitable and/or non-sporulating bacteria for therapeutic administration to a mammalian subject in need thereof. And the composition is produced by generally following the steps of: (a) providing a fecal material obtained from a mammalian donor subject; and (b) subjecting the fecal material to at least one purification treatment or step under conditions such that a population of bacterial spores is produced from the fecal material. The composition is formulated such that a single oral dose contains at least about 1×10⁴ colony forming units of the bacterial spores, and a single oral dose will typically contain about 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, 1×10¹², 1×10¹³, 1×10¹⁴, 1×10¹⁵, or greater than 1×10¹⁵ CFUs of the bacterial spores. The presence and/or concentration of a given type of bacteria or bacterial spore may be known or unknown in a given purified spore population. If known, for example the concentration of bacteria or spores of a given strain, or the aggregate of all strains, is e.g., 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, 1×10¹², 1×10¹³, 1×10¹⁴, 1×10¹⁵, or greater than 1×10¹⁵ viable bacteria or bacterial spores per gram of composition or per administered dose.

In some formulations, the composition contains at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater than 90% spores on a mass basis. In some formulations, the administered dose does not exceed 200, 300, 400, 500, 600, 700, 800, 900 milligrams or 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, or 1.9 grams in mass.

The bacterial compositions are generally formulated for oral or gastric administration, typically to a mammalian subject. In particular embodiments, the composition is formulated for oral administration as a solid, semi-solid, gel, or liquid form, such as in the form of a pill, tablet, capsule, or lozenge. In some embodiments, such formulations contain or are coated by an enteric coating to protect the bacteria through the stomach and small intestine, although spores are generally resistant to the stomach and small intestines.

The bacterial compositions may be formulated to be effective in a given mammalian subject in a single administration or over multiple administrations. For example, a single administration is substantially effective to reduce Cl. difficile and/or Cl. difficile toxin content in a mammalian subject to whom the composition is administered. Substantially effective means that Cl. difficile and/or Cl. difficile toxin content in the subject is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or greater than 99% following administration of the composition.

Kits For Diagnosis of a State of Dysbiosis in a Subject

In some embodiments, the invention includes kits for carrying out methods of the invention described herein and in the claims. In some embodiments, the invention includes a kit for diagnosis of a state of dysbiosis in a mammalian subject in need thereof. In one embodiment, the kit includes a plurality of detection means suitable for use in detecting (1) a first bacterial entity comprising a keystone bacterial entity and (2) a second bacterial entity, wherein the first and second bacterial entities comprise a Network Ecology, as described herein. The kit can include instructions for use of the kit.

In other embodiments, the kit provides detection means, reagents, and instructions for detecting a first bacterial entity and a second bacterial entity that comprise a Network Ecology by: obtaining a fecal sample from a mammalian subject comprising a plurality of bacterial entities, contacting the fecal sample with a first detection moiety (and in some cases, a second detection moiety) capable of detecting the first bacterial entity and the second bacterial entity present in the network, detecting the absence of the first and/or second bacterial entities in the fecal sample, and thereby detecting a dysbiosis in the mammailian subject. In some embodiments, the kit provides reagents and steps for administering to the mammailian subject a composition comprising an effect amount of the first and/or second bacterial species.

In some embodiments, the kit includes detection means and instructions for obtaining a fecal sample from the mammalian subject comprising a plurality of bacterial entities; contacting the fecal sample with a first detection moiety capable of detecting a first bacterial entity present in an network; detecting the absence of the first bacterial entity in the fecal sample, thereby detecting a dysbiosis in the mammalian subject; and administering to the mammalian subject a composition comprising an effective amount of the first bacterial entity.

In other embodiments, the kit includes reagents and instructions for a method for treating, preventing, or reducing the severity of a disorder selected from the group consisting of Clostridium difficile Associated Diarrhea (CDAD), Type 2 Diabetes, Obesity, Irritable Bowel Disease (IBD), colonization with a pathogen or pathobiont, and infection with a drug-resistant pathogen or pathobiont, comprising: administering to a mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria or the purified bacterial preparation capable of forming a network ecology selected from the group consisting of those in claims 1-61 below and described throughout the specification.

In another embodiment, the kit includes reagents and instructions for a method for producing short chain fatty acids (SCFA) within a mammalian subject, comprising: administering to said mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria of the purified bacterial preparation capable of forming one or a plurality of bacterial functional pathways, the one or plurality of bacterial functional pathways capable of forming a functional network ecology selected from the group consisting of those in claims 69-71 and described throughout in the specification.

In another embodiment, the kit includes reagents and instructions for a method for catalyzing secondary metabolism of bile acids within a mammalian subject, comprising: administering to said mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, said therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, the plurality of isolated bacteria of the purified bacterial preparation capable of forming one or a plurality of bacterial functional pathways, the one or plurality of bacterial functional pathways capable of forming a functional network ecology selected from the group consisting of claims 72-74 and throughout the specification.

Systems for Predicting a Dysbiosis in a Subject

The invention provides systems for predicting a dysbiosis in a subject, the system comprising: a storage memory for storing a dataset associated with a sample obtained from the subject, wherein the dataset comprises content data for at least one network of bacterial entities described herein, and a processor communicatively coupled to the storage memory for determining a score with an interpretation function wherein the score is predictive of dysbiosis in the subject.

In some embodiments, the invention provides systems for detecting a dysbiosis in a subject comprising: a storage memory for storing a dataset associated with a sample obtained from the subject, wherein the dataset comprises content data for at least one network of bacterial entities described herein, and a processor communicatively coupled to the storage memory for determining a score with an interpretation function, wherein the score is predictive of dysbiosis in the subject.

An example of a computer system and its components that can be used to perform methods of the invention are described below in FIG. 21.

Computer Overview

FIG. 21 is a high-level block diagram illustrating an example of a computer 2100 for use as a server or a user device, in accordance with one embodiment. Illustrated are at least one processor 2102 coupled to a chipset 2104. The chipset 2104 includes a memory controller hub 2120 and an input/output (I/O) controller hub 2122. A memory 2106 and a graphics adapter 2112 are coupled to the memory controller hub 2120, and a display device 2118 is coupled to the graphics adapter 2112. A storage device 2108, keyboard 2110, pointing device 2114, and network adapter 2116 are coupled to the I/O controller hub 2122. Other embodiments of the computer 2100 have different architectures. For example, the memory 2106 is directly coupled to the processor 2102 in some embodiments.

The storage device 2108 is a non-transitory computer-readable storage medium such as a hard drive, compact disk read-only memory (CD-ROM), DVD, or a solid-state memory device. The memory 2106 holds instructions and data used by the processor 2102. The pointing device 2114 is used in combination with the keyboard 2110 to input data into the computer system 200. The graphics adapter 2112 displays images and other information on the display device 2118. In some embodiments, the display device 2118 includes a touch screen capability for receiving user input and selections. The network adapter 2116 couples the computer system 2100 to the network. Some embodiments of the computer 2100 have different and/or other components than those shown in FIG. 21. For example, the server can be formed of multiple blade servers and lack a display device, keyboard, and other components.

The computer 2100 is adapted to execute computer program modules for providing functionality described herein. As used herein, the term “module” refers to computer program instructions and other logic used to provide the specified functionality. Thus, a module can be implemented in hardware, firmware, and/or software. In one embodiment, program modules formed of executable computer program instructions are stored on the storage device 2108, loaded into the memory 2106, and executed by the processor 2102.

Methods of the Invention

Method of Determining Network Ecologies

Methods are provided for a computational approach based in part on network theory to construct the ecology of a group of microorganisms based on the presence or absence of specific OTUs (i.e., microbial genera, species or strains) in a given set of sampled subjects. See FIG. 16. See e.g., Cormen T H, Leiserson C E, Rivest R L, and Stein C. 2009. Introduction to Algorithms. Third edition. The MIT Press. Garey M R, and Johnson D S. 1979. Computers and Intractability: A Guide to the Theory of NP-Completeness. First Edition. W. H. Freeman. The approach includes the following: (i) identifying the microbial network ecologies that are present in both healthy and diseased subjects, (ii) identifying the keystone OTUs and/or functions (FIG. 17), and phylogenetic clades that characterize a given ecology, and (iii) providing specific metrics with which to prioritize the various network ecologies with respect to their capacity to be useful in restoring the microbiome from a state of dysbiosis to a state of health. In general the method first defines all low and high order networks within given sets of subjects, and then utilizes a comparative approach to define biologically significant networks.

This method comprises computing a co-occurrence matrix of OTUs (i.e., presence or absence) for each subject across a defined subject population (populations are defined by a specific phenotype such as but not limited to “subjects who are healthy”, or “subjects with disease”). The method comprises computing all nodes (OTUs, or species, or strains) and edges (co-occurrence between OTUs, or species, or strains) that define the Network Ecology in a given subject's sample. Each co-occurrence is scored using a discrete binary variable denoting presence or absence. While the algorithm allows co-occurrences to be weighted based on the relative abundance of OTUs in the samples, in general, this is undesirable since low abundance OTUs may be important ecologically. Furthermore, a discretized measure of presence or absence of nodes eliminates bias and errors in the computed network ecologies that will arise from bias in methods used to generate relative abundance measures. A discreet method measuring presence or absence enables the detection of low frequency OTUs and the elucidation of networks that are often missed by methods based on relative abundance measures. Following derivation of all low and high order networks in a given subject, one can define all the network ecologies in a given phenotype (i.e., collections of data sets from subjects with a unifying characteristic, for example, all data sets from healthy subjects) by defining the node and edge combinations that are maximally observed across all subjects. Without being bound by theory, it is understood that such network ecologies are present in a mammalian subject. The algorithm iterates the construction of network ecologies to rank all ecologies (i.e. nodes and edges) within each sample based on co-occurrence, [maximum co-occurrence; maximum co-occurrence less 1; maximum co-occurrence less 2; etc.] until the networks with minimum co-occurrence are defined (i.e., a minimum edge score is achieved). This method can be computationally intensive for data sets containing a large number of subjects. For data sets containing a large number of subjects the algorithm uses a strategy whereby first seed network ecologies are constructed using the method defined above in a subset of subjects and then combinations of these seed networks are used to search for higher order networks across the entire data set.

Biological significance can be assigned to the observed network ecologies and members of a given Network Ecology based on multiple computed metrics including, but not limited to: (i) the frequency that a given OTU or Network Ecology is observed; (ii) the number of OTUs in the network; the frequency of occurrence of the network across subjects (i.e., pervasiveness); (iii) the phylogenetic breadth of the network, (iv) specific functional properties, and (v) whether the network occurs preferentially in individuals that are healthy versus those harboring disease (i.e., the various phenotypes). All network ecologies or OTUs that occur in one phenotype (e.g., health) are compared to those that occur in other phenotypes (e.g., one or more specific disease states) to core Network ecologies or OTUs that are found in one, two, or any multiple of phenotypes. Network ecologies are considered to be related if at least 70%, 80%, or 90% of their OTUs are in common. All network ecologies or OTUs are assigned a score for their biological significance based on but not limited to: (i) the intersections of phenotypes in which they occur or do not occur (e.g. present in health but not disease), and (ii) the various metrics above defined. The final output of all of these steps defines a set of Network Ecologies that are of high biological significance and a set of Keystone OTUs and/or metabolic functions that are integral components of these derived ecologies.

From these Network Ecologies, the method includes defining “Network Classes” that represent network groups or clusters with specific, related compositional characteristics with respect to OTU content, phylogenetic diversity, and metabolic functional capacity (FIG. 18). Network Classes can be first defined by setting an inclusion threshold for networks to include in the analysis that is based on biological characteristics of the networks such as but not limited to the size (number of OTUs) and pervasiveness (i.e., how frequently a given network is observed in a population of individuals). Selected network ecologies are then clustered using two vectors: one vector is phylogenetic relatedness of individual OTUs as defined by a computed phylogenetic tree, and the second vector is network relatedness based on the OTUs content in the individual networks. In another embodiment, clustering vectors are related based on metabolic functional pathways harbored by individual OTUs, and network relatedness is based on the functional pathways present in each individual network. Network Classes are defined by specific nodes in the dendrogram representing the computed network relatedness, and each class is characterized by a specific combination of OTUs. In one embodiment, these nodes are defined as branches of the hierarchical clustering tree based on the topological overlap measure; this measure is a highly robust measure of network interconnectedness. See Langfelder P, Zhang B, Horvath S. 2008. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24: 719-720.

From these Networks Classes, a target microbial composition's usefulness, e.g., as a therapeutic, is selected using desired phylogenetic and functional properties for subsequent testing in in vitro and in vivo models. Exemplary Network Classes are delineated in Table 12, and Table 13 defines taxonomic families that are characteristic of Network Classes.

As described herein, provided are compositions (Table 8) containing keystone OTUs for states of health, including one or more of the OTUs provided below in Table 9.

As described herein, provided are compositions containing keystone OTUs, keystone metabolic functions and, optionally, non-keystone OTUs, including one or more of the OTUs provided below in Table 10.

In some therapeutic compositions, keystone OTUs are provided from members of a genera or family selected from Table 9.

Exemplary network ecologies are provided in Table 8, Table 11, Table 12, Table 14a 14b, and 14c, and Table 17.

Exemlary functional network ecologies are provided in Table 18 and Table 21.

Thus, provided herein are methods for production of a composition containing a population of bacteria as either vegetative cells or spores or both, suitable for therapeutic administration to a mammalian subject in need thereof. The composition is produced by generally following the steps of: (a) defining a target composition by selecting a Network Ecology, Functional Network Ecology, a Network Class, or a set of Keystone OTUs or Keystone Metabolic Functions that comprise the Network Ecology or Functional Network Ecology of interest (a) providing bacterial OTUs obtained from one or more bacterial cultures, biological or environmental sources, or a mammalian donor subject; and (b) combining the bacterial OTUs in a ratio and an amount sufficient to form a Network Ecology or Functional Network Ecology. The composition is formulated such that a single oral dose contains at least about 1×10⁴ colony forming units of the bacteria, and a single oral dose will typically contain about 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, 1×10¹², 1×10¹³, 1×10¹⁴, 1×10¹⁵, or greater than 1×10¹⁵ CFUs of the bacteria. The concentration of bacterial of a given species or strain, or the aggregate of all species or strains, is e.g., 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, 1×10¹², 1×10¹³, 1×10¹⁴, 1×10¹⁵, or greater than 1×10¹⁵ viable bacteria per gram of composition or per administered dose.

The bacterial compositions are generally formulated for oral or gastric administration, typically to a mammalian subject. In particular embodiments, the composition is formulated for oral administration as a solid, semi-solid, gel, or liquid form, such as in the form of a pill, tablet, capsule, or lozenge. In some embodiments, such formulations contain or are coated by an enteric coating to protect the bacteria through the stomach and small intestine, although compositions containing spores are generally resistant to the environment of the stomach and small intestine. Alternatively, the bacterial composition may be formulated for naso-gastric or rectal administration.

The bacterial compositions may be formulated to be effective in a given mammalian subject in a single administration or over multiple administrations. For example, a single administration is substantially effective to reduce Clostridium difficile (i.e., C. difficile) and/or C. difficile toxin content and/or toxin activity, in a mammalian subject to whom the composition is administered. Substantially effective means that Cl. difficile and/or C. difficile toxin content in the subject is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or greater than 99% following administration of the composition.

Methods for Determining 16S Sequences

OTUs can be defined either by full 16S sequencing of the rRNA gene, by sequencing of a specific hypervariable region of this gene (i.e. V1, V2, V3, V4, V5, V6, V7, V8, or V9), or by sequencing of any combination of hypervariable regions from this gene (e.g. V1-3 or V3-5). The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most microbes.

Using well known techniques, in order to determine the full 16S sequence or the sequence of any hypervariable region of the 16S sequence, genomic DNA is extracted from a bacterial sample, the 16S rDNA (full region or specific hypervariable regions) amplified using polymerase chain reaction (PCR), the PCR products cleaned, and nucleotide sequences delineated to determine the genetic composition of 16S gene or subdomain of the gene. If full 16S sequencing is performed, the sequencing method used may be, but is not limited to, Sanger sequencing. If one or more hypervariable regions are used, such as the V4 region, the sequencing can be, but is not limited to being, performed using the Sanger method or using a next-generation sequencing method, such as an Illumina (sequencing by synthesis) method using barcoded primers allowing for multiplex reactions.

OTUs can be defined by a combination of nucleotide markers or genes, in particular highly conserved genes (e.g., “house-keeping” genes), or a combination thereof, full-genome sequence, or partial genome sequence generated using amplified genetic products, or whole genome sequence (WGS). Using well defined methods DNA extracted from a bacterial sample will have specific genomic regions amplified using PCR and sequenced to determine the nucleotide sequence of the amplified products. In the whole genome shotgun (WGS) method, extracted DNA will be directly sequenced without amplification. Sequence data can be generated using any sequencing technology including, but not limited to Sanger, Illumina, 454 Life Sciences, Ion Torrent, ABI, Pacific Biosciences, and/or Oxford Nanopore.

Methods for Preparing a Bacterial Composition for Administration to a Subject

Methods for producing bacterial compositions can include three main processing steps, combined with one or more mixing steps. The steps include organism banking, organism production, and preservation.

For banking, the strains included in the bacterial composition may be (1) isolated directly from a specimen or taken from a banked stock, (2) optionally cultured on a nutrient agar or broth that supports growth to generate viable biomass, and (3) the biomass optionally preserved in multiple aliquots in long-term storage.

In embodiments that use a culturing step, the agar or broth can contain nutrients that provide essential elements and specific factors that enable growth. An example would be a medium composed of 20 g/L glucose, 10 g/L yeast extract, 10 g/L soy peptone, 2 g/L citric acid, 1.5 g/L sodium phosphate monobasic, 100 mg/L ferric ammonium citrate, 80 mg/L magnesium sulfate, 10 mg/L hemin chloride, 2 mg/L calcium chloride, 1 mg/L menadione. A variety of microbiological media and variations are well known in the art (e.g. R. M. Atlas, Handbook of Microbiological Media (2010) CRC Press). Medium can be added to the culture at the start, may be added during the culture, or may be intermittently/continuously flowed through the culture. The strains in the bacterial composition may be cultivated alone, as a subset of the bacterial composition, or as an entire collection comprising the bacterial composition. As an example, a first strain may be cultivated together with a second strain in a mixed continuous culture, at a dilution rate lower than the maximum growth rate of either cell to prevent the culture from washing out of the cultivation.

The inoculated culture is incubated under favorable conditions for a time sufficient to build biomass. For bacterial compositions for human use, this is often at 37° C. temperature, pH, and other parameter with values similar to the normal human niche. The environment can be actively controlled, passively controlled (e.g., via buffers), or allowed to drift. For example, for anaerobic bacterial compositions (e.g., gut microbiota), an anoxic/reducing environment can be employed. This can be accomplished by addition of reducing agents such as cysteine to the broth, and/or stripping it of oxygen. As an example, a culture of a bacterial composition can be grown at 37° C., pH 7, in the medium above, pre-reduced with 1 g/L cysteine □HCl.

When the culture has generated sufficient biomass, it can be preserved for banking. The organisms can be placed into a chemical milieu that protects from freezing (adding ‘cryoprotectants’), drying (‘lyoprotectants’), and/or osmotic shock (‘osmoprotectants’), dispensing into multiple (optionally identical) containers to create a uniform bank, and then treating the culture for preservation. Containers are generally impermeable and have closures that assure isolation from the environment. Cryopreservation treatment is accomplished by freezing a liquid at ultra-low temperatures (e.g., at or below −80° C.). Dried preservation removes water from the culture by evaporation (in the case of spray drying or ‘cool drying’) or by sublimation (e.g., for freeze drying, spray freeze drying). Removal of water improves long-term bacterial composition storage stability at temperatures elevated above cryogenic. If the bacterial composition comprises spore forming species and results in the production of spores, the final composition can be purified by additional means, such as density gradient centrifugation preserved using the techniques described above. Bacterial composition banking can be done by culturing and preserving the strains individually, or by mixing the strains together to create a combined bank. As an example of cryopreservation, a bacterial composition culture can be harvested by centrifugation to pellet the cells from the culture medium, the supernate decanted and replaced with fresh culture broth containing 15% glycerol. The culture can then be aliquoted into 1 mL cryotubes, sealed, and placed at −80° C. for long-term viability retention. This procedure achieves acceptable viability upon recovery from frozen storage.

Organism production can be conducted using similar culture steps to banking, including medium composition and culture conditions. It can be conducted at larger scales of operation, especially for clinical development or commercial production. At larger scales, there can be several subcultivations of the bacterial composition prior to the final cultivation. At the end of cultivation, the culture is harvested to enable further formulation into a dosage form for administration. This can involve concentration, removal of undesirable medium components, and/or introduction into a chemical milieu that preserves the bacterial composition and renders it acceptable for administration via the chosen route. For example, a bacterial composition can be cultivated to a concentration of 10¹⁰ CFU/mL, then concentrated 20-fold by tangential flow microfiltration; the spent medium can be exchanged by diafiltering with a preservative medium consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium phosphate buffer. The suspension can then be freeze-dried to a powder and titrated.

After drying, the powder can be blended to an appropriate potency, and mixed with other cultures and/or a filler such as microcrystalline cellulose for consistency and ease of handling, and the bacterial composition formulated as provided herein.

Methods of Treating a Subject

In some embodiments, the compositions disclosed herein are administered to a patient or a user (sometimes collectively referred to as a “subject”). As used herein “administer” and “administration” encompasses embodiments in which one person directs another to consume a bacterial composition in a certain manner and/or for a certain purpose, and also situations in which a user uses a bacteria composition in a certain manner and/or for a certain purpose independently of or in variance to any instructions received from a second person. Non-limiting examples of embodiments in which one person directs another to consume a bacterial composition in a certain manner and/or for a certain purpose include when a physician prescribes a course of conduct and/or treatment to a patient, when a parent commands a minor user (such as a child) to consume a bacterial composition, when a trainer advises a user (such as an athlete) to follow a particular course of conduct and/or treatment, and when a manufacturer, distributer, or marketer recommends conditions of use to an end user, for example through advertisements or labeling on packaging or on other materials provided in association with the sale or marketing of a product.

The bacterial compositions offer a protective and/or therapeutic effect against diseases, disorders or conditions associated with dysbiosis of the gut microbiota, including but not limited to metabolic disorders such as pre-diabetes, type 1 diabetes, type 2 diabetes, obesity and non-alcoholic fatty liver disease (NAFLD), gastrointestinal disorders such as inflammatory bowel disease (IBD, such as ulcerative colitis and Crohns' disease), pouchitis and irritable bowel syndrome (IBS), and infectious diseases as described herein.

In some embodiments, the bacterial compositions offer a protective and/or therapeutic effect against diseases, disorders or conditions associated with dysbiosis of the gut microbiota, including but not limited to, metabolic diseases (e.g., Type 1 diabetes, Type 2 diabetes, Gestational diabetes, Diabetes complications, Prediabetes, NAFLD/NASH, Obesity, Weight Loss), GI diseases (Inflammatory bowel disease (IBD), Irritable bowel syndrome (IBS), Ulcerative Colitis, Crohn's Disease). Infectious diseases (Clostridium difficile Associated Diarrhea (CDAD), Carbapenem-resistant Enterobacteriaceae (CRE), Multidrug-resistant Acinetobacter, Drug-resistant Campylobacter, Extended spectrum β-lactamase producing Enterobacteriaceae (ESBLs), Vancomycin-resistant Enterococcus (VRE), Multidrug-resistant Pseudomonas aeruginosa, Drug-resistant Non-typhoidal Salmonella, Drug-resistant Salmonella Typhi, Drug-resistant Shigella, Methicillin-resistant Staphylococcus aureus (MRSA), Drug-resistant Streptococcus pneumonia, Vancomycin-resistant Staphylococcus aureus (VRSA), Erythromycin-resistant Group A Streptococcus, Clindamycin-resistant Group B Streptococcus, Pathogenic fungus, or Candida infection).

The present bacterial compositions can be administered to animals, including humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs, turkeys, chickens), and household pets (e.g., dogs, cats, rodents).

In the present method, the bacterial composition can be administered enterically, in other words, by a route of access to the gastrointestinal tract. This includes oral administration, rectal administration (including enema, suppository, or colonoscopy), by an oral or nasal tube (nasogastric, nasojejunal, oral gastric, or oral jejunal), as detailed more fully herein.

Pretreatment Protocols

Prior to administration of the bacterial composition, the patient can optionally have a pretreatment protocol to prepare the gastrointestinal tract to receive the bacterial composition.

As one way of preparing the patient for administration of the microbial ecosystem, at least one antibiotic can be administered to alter the bacteria in the patient. As another way of preparing the patient for administration of the microbial ecosystem, a standard colon-cleansing preparation can be administered to the patient to substantially empty the contents of the colon, such as used to prepare a patient for a colonscopy. By “substantially emptying the contents of the colon,” this application means removing at least 75%, at least 80%, at least 90%, at least 95%, or about 100% of the contents of the ordinary volume of colon contents. Antibiotic treatment can precede the colon-cleansing protocol.

If a patient has received an antibiotic for treatment of an infection, or if a patient has received an antibiotic as part of a specific pretreatment protocol, in one embodiment, the antibiotic can be stopped in sufficient time to allow the antibiotic to be substantially reduced in concentration in the gut before the bacterial composition is administered. In one embodiment, the antibiotic can be discontinued 1, 2, or 3 days before the administration of the bacterial composition. In another embodiment, the antibiotic can be discontinued 3, 4, 5, 6, or 7 antibiotic half-lives before administration of the bacterial composition. In another embodiment, the antibiotic can be chosen so the constituents in the bacterial composition have an MIC50 that is higher than the concentration of the antibiotic in the gut.

MIC50 of a bacterial composition or the elements in the composition can be determined by methods well known in the art. Reller et al., Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices, Clinical Infectious Diseases 49(11):1749-1755 (2009). In such an embodiment, the additional time between antibiotic administration and administration of the bacterial composition is not necessary. If the pretreatment protocol is part of treatment of an acute infection, the antibiotic can be chosen so that the infection is sensitive to the antibiotic, but the constituents in the bacterial composition are not sensitive to the antibiotic.

Administration of Bacterial Compositions

The bacterial compositions of the invention are suitable for administration to mammals and non-mammalian animals in need thereof. In certain embodiments, the mammalian subject is a human subject who has one or more symptoms of a dysbiosis.

When the mammalian subject is suffering from a disease, disorder or condition characterized by an aberrant microbiota, the bacterial compositions described herein are suitable for treatment thereof. In some embodiments, the mammalian subject has not received antibiotics in advance of treatment with the bacterial compositions. For example, the mammalian subject has not been administered at least two doses of vancomycin, metronidazole and/or or similar antibiotic compound within one week prior to administration of the therapeutic composition. In other embodiments, the mammalian subject has not previously received an antibiotic compound in the one month prior to administration of the therapeutic composition. In other embodiments, the mammalian subject has received one or more treatments with one or more different antibiotic compounds and such treatment(s) resulted in no improvement or a worsening of symptoms.

In some embodiments, the gastrointestinal disease, disorder or condition is diarrhea caused by C. difficile including recurrent C. difficile infection, ulcerative colitis, colitis, Crohn's disease, or irritable bowel disease. Beneficially, the therapeutic composition is administered only once prior to improvement of the disease, disorder or condition. In some embodiments the therapeutic composition is administered at intervals greater than two days, such as once every three, four, five or six days, or every week or less frequently than every week. Or the preparation may be administered intermittently according to a set schedule, e.g., once a day, once weekly, or once monthly, or when the subject relapses from the primary illness. In another embodiment, the preparation may be administered on a long-term basis to subjects who are at risk for infection with or who may be carriers of these pathogens, including subjects who will have an invasive medical procedure (such as surgery), who will be hospitalized, who live in a long-term care or rehabilitation facility, who are exposed to pathogens by virtue of their profession (livestock and animal processing workers), or who could be carriers of pathogens (including hospital workers such as physicians, nurses, and other health care professionals).

In embodiments, the bacterial composition is administered enterically. This preferentially includes oral administration, or by an oral or nasal tube (including nasogastric, nasojejunal, oral gastric, or oral jejunal). In other embodiments, administration includes rectal administration (including enema, suppository, or colonoscopy). The bacterial composition may be administered to at least one region of the gastrointestinal tract, including the mouth, esophagus, stomach, small intestine, large intestine, and rectum. In some embodiments it is administered to all regions of the gastrointestinal tract. The bacterial compositions may be administered orally in the form of medicaments such as powders, capsules, tablets, gels or liquids. The bacterial compositions may also be administered in gel or liquid form by the oral route or through a nasogastric tube, or by the rectal route in a gel or liquid form, by enema or instillation through a colonoscope or by a suppository.

If the composition is administered colonoscopically and, optionally, if the bacterial composition is administered by other rectal routes (such as an enema or suppository) or even if the subject has an oral administration, the subject may have a colon cleansing preparation. The colon-cleansing preparation can facilitate proper use of the colonoscope or other administration devices, but even when it does not serve a mechanical purpose it can also maximize the proportion of the bacterial composition relative to the other organisms previously residing in the gastrointestinal tract of the subject. Any ordinarily acceptable colon cleansing preparation may be used such as those typically provided when a subject undergoes a colonoscopy.

Dosages and Schedule for Administration

In some embodiments, the bacteria and bacterial compositions are provided in a dosage form. In certain embodiments, the dosage form is designed for administration of at least one OTU or combination thereof disclosed herein, wherein the total amount of bacterial composition administered is selected from 0.1 ng to 10 g, 10 ng to 1 g, 100 ng to 0.1 g, 0.1 mg to 500 mg, 1 mg to 100 mg, or from 10-15 mg. In other embodiments, the bacterial composition is consumed at a rate of from 0.1 ng to 10 g a day, 10 ng to 1 g a day, 100 ng to 0.1 g a day, 0.1 mg to 500 mg a day, 1 mg to 100 mg a day, or from 10-15 mg a day, or more.

In certain embodiments, the treatment period is at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, or at least 1 year. In some embodiments the treatment period is from 1 day to 1 week, from 1 week to 4 weeks, from 1 month, to 3 months, from 3 months to 6 months, from 6 months to 1 year, or for over a year.

In one embodiment, 10⁵ and 10¹² microorganisms total can be administered to the patient in a given dosage form. In another embodiment, an effective amount can be provided in from 1 to 500 ml or from 1 to 500 grams of the bacterial composition having from 10⁷ to 10¹¹ bacteria per ml or per gram, or a capsule, tablet or suppository having from 1 mg to 1000 mg lyophilized powder having from 10⁷ to 10¹¹ bacteria. Those receiving acute treatment can receive higher doses than those who are receiving chronic administration.

Any of the preparations described herein can be administered once on a single occasion or on multiple occasions, such as once a day for several days or more than once a day on the day of administration (including twice daily, three times daily, or up to five times daily). In another embodiment, the preparation can be administered intermittently according to a set schedule, e.g., once weekly, once monthly, or when the patient relapses from the primary illness. In one embodiment, the preparation can be administered on a long-term basis to individuals who are at risk for infection with or who may be carriers of these pathogens.

Patient Selection

Particular bacterial compositions can be selected for individual patients or for patients with particular profiles. For example, 16S sequencing can be performed for a given patient to identify the bacteria present in his or her microbiota. The sequencing can either profile the patient's entire microbiome using 16S sequencing (to the family, genera, or species level), a portion of the patient's microbiome using 16S sequencing, or it can be used to detect the presence or absence of specific candidate bacteria that are biomarkers for health or a particular disease state. Based on the biomarker data, a particular composition can be selected for administration to a patient to supplement or complement a patient's microbiota in order to restore health or treat or prevent disease. In another embodiment, patients can be screened to determine the composition of their microbiota to determine the likelihood of successful treatment.

Combination Therapy

The bacterial compositions can be administered with other agents in a combination therapy mode, including anti-microbial agents and prebiotics. Administration can be sequential, over a period of hours or days, or simultaneous.

In one embodiment, the bacterial compositions are included in combination therapy with one or more anti-microbial agents, which include anti-bacterial agents, anti-fungal agents, anti-viral agents and anti-parasitic agents.

Anti-bacterial agents can include cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cefamandole, cefoxitin, cefprozil, and ceftobiprole); fluoroquinolone antibiotics (cipro, Levaquin, floxin, tequin, avelox, and norflox); tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); penicillin antibiotics (amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin); and carbapenem antibiotics (ertapenem, doripenem, imipenem/cilastatin, and meropenem).

Anti-viral agents can include Abacavir, Acyclovir, Adefovir, Amprenavir, Atazanavir, Cidofovir, Darunavir, Delavirdine, Didanosine, Docosanol, Efavirenz, Elvitegravir, Emtricitabine, Enfuvirtide, Etravirine, Famciclovir, Foscarnet, Fomivirsen, Ganciclovir, Indinavir, Idoxuridine, Lamivudine, Lopinavir Maraviroc, MK-2048, Nelfinavir, Nevirapine, Penciclovir, Raltegravir, Rilpivirine, Ritonavir, Saquinavir, Stavudine, Tenofovir Trifluridine, Valaciclovir, Valganciclovir, Vidarabine, Ibacitabine, Amantadine, Oseltamivir, Rimantidine, Tipranavir, Zalcitabine, Zanamivir and Zidovudine.

Examples of antifungal compounds include, but are not limited to polyene antifungals such as natamycin, rimocidin, filipin, nystatin, amphotericin B, candicin, and hamycin; imidazole antifungals such as miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, and tioconazole; triazole antifungals such as fluconazole, itraconazole, isavuconazole, ravuconazole, posaconazole, voriconazole, terconazole, and albaconazole; thiazole antifungals such as abafungin; allylamine antifungals such as terbinafine, naftifine, and butenafine; and echinocandin antifungals such as anidulafungin, caspofungin, and micafungin. Other compounds that have antifungal properties include, but are not limited to polygodial, benzoic acid, ciclopirox, tolnaftate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprogin.

In one embodiment, the bacterial compositions are included in combination therapy with one or more corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, immunosuppressive drugs, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anti-cholinergic drugs for rhinitis, anti-cholinergic decongestants, mast-cell stabilizers, monoclonal anti-IgE antibodies, vaccines, and combinations thereof.

A prebiotic is a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health. Prebiotics can include complex carbohydrates, amino acids, peptides, or other essential nutritional components for the survival of the bacterial composition. Prebiotics include, but are not limited to, amino acids, biotin, fructooligosaccharide, galactooligosaccharides, inulin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, and xylooligosaccharides.

Methods for Testing Bacterial Compositions for Populating Effect

In Vivo Assay for Determining Whether a Bacterial Composition Populates a Subject's Gastrointestinal Tract

In order to determine that the bacterial composition populates the gastrointestinal tract of a subject, an animal model, such as a mouse model, can be used. The model can begin by evaluating the microbiota of the mice. Qualitative assessments can be accomplished using 16S profiling of the microbial community in the feces of normal mice. It can also be accomplished by full genome sequencing, whole genome shotgun sequencing (WGS), or traditional microbiological techniques. Quantitative assessments can be conducted using quantitative PCR (qPCR), described below, or by using traditional microbiological techniques and counting colony formation.

Optionally, the mice can receive an antibiotic treatment to mimic the condition of dysbiosis. Antibiotic treatment can decrease the taxonomic richness, diversity, and evenness of the community, including a reduction of abundance of a significant number of bacterial taxa. Dethlefsen et al., The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing, PLoS Biology 6(11):3280 (2008). At least one antibiotic can be used, and antibiotics are well known. Antibiotics can include aminoglycoside antibiotic (amikacin, arbekacin, gentamicin, kanamycin, neomycin, netilmicin, paromomycin, rhodostreptomycin, streptomycin, tobramycin, and apramycin), amoxicillin, ampicillin, Augmentin (an amoxicillin/clavulanate potassium combination), cephalosporin (cefaclor, defadroxil, cefazolin, cefixime, fefoxitin, cefprozil, ceftazimdime, cefuroxime, cephalexin), clavulanate potassium, clindamycin, colistin, gentamycin, kanamycin, metronidazole, or vancomycin. As an individual, nonlimiting specific example, the mice can be provided with drinking water containing a mixture of the antibiotics kanamycin, colistin, gentamycin, metronidazole and vancomycin at 40 mg/kg, 4.2 mg/kg, 3.5 mg/kg, 21.5 mg/kg, and 4.5 mg/kg (mg per average mouse body weight), respectively, for 7 days. Alternatively, mice can be administered ciprofloxacin at a dose of 15-20 mg/kg (mg per average mouse body weight), for 7 days. If the mice are provided with an antibiotic, a wash out period of from one day to three days may be provided with no antibiotic treatment and no bacterial composition treatment.

Subsequently, the bacterial composition is administered to the mice by oral gavage. The bacterial composition may be administered in a volume of 0.2 ml containing 10⁴ CFUs of each type of bacteria in the bacterial composition. Dose-response may be assessed by using a range of doses, including, but not limited to 10², 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, and/or 10¹⁰.

The mice can be evaluated using 16S sequencing, full genome sequencing, whole genome shotgun sequencing (WGS), or traditional microbiological techniques to determine whether the bacterial composition has populated the gastrointestinal tract of the mice. For example only, one day, three days, one week, two weeks, and one month after administration of the bacterial composition to the mice, 16S profiling is conducted to determine whether the test bacterial composition has populated the gastrointestinal tract of the mice. Quantitative assessments, including qPCR and traditional microbiological techniques such as colony counting, can additionally or alternatively be performed, at the same time intervals.

Furthermore, the number of sequence counts that correspond exactly to those in the bacterial composition over time can be assessed to determine specifically which components of the bacterial composition reside in the gastrointestinal tract over a particular period of time. In one embodiment, the strains of the bacterial composition persist for a desired period of time. In another embodiment, the components of the bacterial composition persist for a desired period of time, while also increasing the ability of other microbes (such as those present in the environment, food, etc.) to populate the gastrointestinal tract, further increasing overall diversity, as discussed below.

Ability of Bacterial compositions to Populate Different Regions of the Gastrointestinal Tract

The present bacterial compositions can also be assessed for their ability to populate different regions of the gastrointestinal tract. In one embodiment, a bacterial composition can be chosen for its ability to populate one or more than one region of the gastrointestinal tract, including, but not limited to the stomach, the small intestine (duodenum, jejunum, and ileum), the large intestine (the cecum, the colon (the ascending, transverse, descending, and sigmoid colon), and the rectum).

An in vivo study can be conducted to determine which regions of the gastrointestinal tract a given bacterial composition will populate. A mouse model similar to the one described above can be conducted, except instead of assessing the feces produced by the mice, particular regions of the gastrointestinal tract can be removed and studied individually. For example, at least one particular region of the gastrointestinal tract can be removed and a qualitative or quantitative determination can be performed on the contents of that region of the gastrointestinal tract. In another embodiment, the contents can optionally be removed and the qualitative or quantitative determination may be conducted on the tissue removed from the mouse.

qPCR

As one quantitative method for determining whether a bacterial composition populates the gastrointestinal tract, quantitative PCR (qPCR) can be performed. Standard techniques can be followed to generate a standard curve for the bacterial composition of interest, either for all of the components of the bacterial composition collectively, individually, or in subsets (if applicable). Genomic DNA can be extracted from samples using commercially-available kits, such as the Mo Bio Powersoil®-htp 96 Well Soil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), the Mo Bio Powersoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), or the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia, Calif.) according to the manufacturer's instructions.

In some embodiments, qPCR can be conducted using HotMasterMix (5PRIME, Gaithersburg, Md.) and primers specific for the bacterial composition of interest, and may be conducted on a MicroAmpx Fast Optical 96-well Reaction Plate with Barcode (0.1 mL) (Life Technologies, Grand Island, N.Y.) and performed on a BioRad C1000™ Thermal Cycler equipped with a CFX96™ Real-Time System (BioRad, Hercules, Calif.), with fluorescent readings of the FAM and ROX channels. The Cq value for each well on the FAM channel is determined by the CFX Manager™ software version 2.1. The log₁₀(cfu/ml) of each experimental sample is calculated by inputting a given sample's Cq value into linear regression model generated from the standard curve comparing the Cq values of the standard curve wells to the known log₁₀(cfu/ml) of those samples. The skilled artisan may employ alternative qPCR modes.

Methods for Characterization of Bacterial Compositions

In certain embodiments, provided are methods for testing certain characteristics of bacterial compositions. For example, the sensitivity of bacterial compositions to certain environmental variables is determined, e.g., in order to select for particular desirable characteristics in a given composition, formulation and/or use. For example, the constituents in the bacterial composition can be tested for pH resistance, bile acid resistance, and/or antibiotic sensitivity, either individually on a constituent-by-constituent basis or collectively as a bacterial composition comprised of multiple bacterial constituents (collectively referred to in this section as bacterial composition).

pH Sensitivity Testing

If a bacterial composition will be administered other than to the colon or rectum (i.e., for example, an oral route), optionally testing for pH resistance enhances the selection of bacterial compositions that will survive at the highest yield possible through the varying pH environments of the distinct regions of the GI tract. Understanding how the bacterial compositions react to the pH of the GI tract also assists in formulation, so that the number of bacteria in a dosage form can be increased if beneficial and/or so that the composition may be administered in an enteric-coated capsule or tablet or with a buffering or protective composition. As the pH of the stomach can drop to a pH of 1 to 2 after a high-protein meal for a short time before physiological mechanisms adjust it to a pH of 3 to 4 and often resides at a resting pH of 4 to 5, and as the pH of the small intestine can range from a pH of 6 to 7.4, bacterial compositions can be prepared that survive these varying pH ranges (specifically wherein at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or as much as 100% of the bacteria can survive gut transit times through various pH ranges). This can be tested by exposing the bacterial composition to varying pH ranges for the expected gut transit times through those pH ranges. Therefore, as a nonlimiting example only, 18-hour cultures of bacterial compositions can be grown in standard media, such as gut microbiota medium (“GMM”, see Goodman et al., Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice, PNAS 108(15):6252-6257 (2011)) or another animal-products-free medium, with the addition of pH adjusting agents for a pH of 1 to 2 for 30 minutes, a pH of 3 to 4 for 1 hour, a pH of 4 to 5 for 1 to 2 hours, and a pH of 6 to 7.4 for 2.5 to 3 hours. An alternative method for testing stability to acid is described in U.S. Pat. No. 4,839,281. Survival of bacteria may be determined by culturing the bacteria and counting colonies on appropriate selective or non-selective media.

Bile Acid Sensitivity Testing

Additionally, in some embodiments, testing for bile-acid resistance enhances the selection of bacterial compositions that will survive exposures to bile acid during transit through the GI tract. Bile acids are secreted into the small intestine and can, like pH, affect the survival of bacterial compositions. This can be tested by exposing the bacterial compositions to bile acids for the expected gut exposure time to bile acids. For example, bile acid solutions can be prepared at desired concentrations using 0.05 mM Tris at pH 9 as the solvent. After the bile acid is dissolved, the pH of the solution may be adjusted to 7.2 with 10% HCl. Bacterial compositions can be cultured in 2.2 ml of a bile acid composition mimicking the concentration and type of bile acids in the patient, 1.0 ml of 10% sterile-filtered feces media and 0.1 ml of an 18-hour culture of the given strain of bacteria. Incubations may be conducted for from 2.5 to 3 hours or longer. An alternative method for testing stability to bile acid is described in U.S. Pat. No. 4,839,281. Survival of bacteria can be determined by culturing the bacteria and counting colonies on appropriate selective or non-selective media.

Antibiotic Sensitivity Testing

As a further optional sensitivity test, bacterial compositions can be tested for sensitivity to antibiotics. In one embodiment, bacterial compositions can be chosen so that the bacterial constituents are sensitive to antibiotics such that if necessary they can be eliminated or substantially reduced from the patient's gastrointestinal tract by at least one antibiotic targeting the bacterial composition.

Adherence to Gastrointestinal Cells

The bacterial compositions may optionally be tested for the ability to adhere to gastrointestinal cells. A method for testing adherence to gastrointestinal cells is described in U.S. Pat. No. 4,839,281.

Methods for Purifying Spores

Solvent Treatments

To purify the bacterial spores, the fecal material is subjected to one or more solvent treatments. A solvent treatment is a miscible solvent treatment (either partially miscible or fully miscible) or an immiscible solvent treatment. Miscibility is the ability of two liquids to mix with each to form a homogeneous solution. Water and ethanol, for example, are fully miscible such that a mixture containing water and ethanol in any ratio will show only one phase. Miscibility is provided as a wt/wt %, or weight of one solvent in 100 g of final solution. If two solvents are fully miscible in all proportions, their miscibility is 100%. Provided as fully miscible solutions with water are alcohols, e.g., methanol, ethanol, isopropanol, butanol, etc. The alcohols can be provided already combined with water; e.g., a solution containing 10%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 89%, 85%, 90%, 95% or greater than 95% Other solvents are only partially miscible, meaning that only some portion will dissolve in water. Diethyl ether, for example, is partially miscible with water. Up to 7 grams of diethyl ether will dissolve in 93 g of water to give a 7% (wt/wt %) solution. If more diethyl ether is added, a two phase solution will result with a distinct diethyl ether layer above the water. Other miscible materials include ethers, dimethoxyethane, or tetrahydrofuran In contrast, an oil such as an alkane and water are immiscible and form two phases. Further, immiscible treatments are optionally combined with a detergent, either an ionic detergent or a non-ionic detergent. Exemplary detergents include Triton X-100, Tween 20, Tween 80, Nonidet P40, a pluronic, or a polyol.

Chromatography Treatments

To purify spore populations, the fecal materials are subjected to one or more chromatographic treatments, either sequentially or in parallel. In a chromatographic treatment, a solution containing the fecal material is contacted with a solid medium containing a hydrophobic interaction chromatographic (HIC) medium or an affinity chromatographic medium. In an alternative embodiment, a solid medium capable of absorbing a residual habitat product present in the fecal material is contacted with a solid medium that adsorbs a residual habitat product. In certain embodiments, the HIC medium contains sepharose or a derivatized sepharose such as butyl sepharose, octyl sepharose, phenyl sepharose, or butyl-s sepharose. In other embodiments, the affinity chromatographic medium contains material derivatized with mucin type I, II, III, IV, V, or VI, or oligosaccharides derived from or similar to those of mucins type I, II, III, IV, V, or VI. Alternatively, the affinity chromatographic medium contains material derivatized with antibodies that recognize spore-forming bacteria.

Mechanical Treatments

Provided herein is the physical disruption of the fecal material, particularly by one or more mechanical treatment such as blending, mixing, shaking, vortexing, impact pulverization, and sonication. As provided herein, the mechanical disrupting treatment substantially disrupts a non-spore material present in the fecal material and does not substantially disrupt a spore present in the fecal material. Mechanical treatments optionally include filtration treatments, where the desired spore populations are retained on a filter while the undesirable (non-spore) fecal components to pass through, and the spore fraction is then recovered from the filter medium. Alternatively, undesirable particulates and eukaryotic cells may be retained on a filter while bacterial cells including spores pass through. In some embodiments the spore fraction retained on the filter medium is subjected to a diafiltration step, wherein the retained spores are contacted with a wash liquid, typically a sterile saline-containing solution or other diluent, in order to further reduce or remove the undesirable fecal components.

Thermal Treatments

Provided herein is the thermal disruption of the fecal material. Generally, the fecal material is mixed in a saline-containing solution such as phosphate-buffered saline (PBS) and subjected to a heated environment, such as a warm room, incubator, water-bath, or the like, such that efficient heat transfer occurs between the heated environment and the fecal material. Preferably the fecal material solution is mixed during the incubation to enhance thermal conductivity and disrupt particulate aggregates. Thermal treatments can be modulated by the temperature of the environment and/or the duration of the thermal treatment. For example, the fecal material or a liquid comprising the fecal material is subjected to a heated environment, e.g., a hot water bath of at least about 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or greater than 100 degrees Celsius, for at least about 1, 5, 10, 15, 20, 30, 45 seconds, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, or 50 minutes, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 hours. In certain embodiments the thermal treatment occurs at two different temperatures, such as 30 seconds in a 100 degree Celsius environment followed by 10 minutes in a 50 degree Celsius environment. In preferred embodiments the temperature and duration of the thermal treatment are sufficient to kill or remove pathogenic materials while not substantially damaging or reducing the germination-competency of the spores.

Irradiation Treatments

Provided are methods of treating the fecal material or separated contents of the fecal material with ionizing radiation, typically gamma irradiation, ultraviolet irradiation or electron beam irradiation provided at an energy level sufficient to kill pathogenic materials while not substantially damaging the desired spore populations. For example, ultraviolet radiation at 254 nm provided at an energy level below about 22,000 microwatt seconds per cm² will not generally destroy desired spores.

Centrifugation and Density Separation Treatments

Provided are methods of separating desired spore populations from the other components of the fecal material by centrifugation. A solution containing the fecal material is subjected to one or more centrifugation treatments, e.g., at about 1000×g, 2000×g, 3000×g, 4000×g, 5000×g, 6000×g, 7000×g, 8000×g or greater than 8000×g. Differential centrifugation separates desired spores from undesired non-spore material; at low forces the spores are retained in solution, while at higher forces the spores are pelleted while smaller impurities (e.g., virus particles, phage) are retained in solution. For example, a first low force centrifugation pellets fibrous materials; a second, higher force centrifugation pellets undesired eukaryotic cells, and a third, still higher force centrifugation pellets the desired spores while small contaminants remain in suspension. In some embodiments density or mobility gradients or cushions (e.g., step cushions), such as Percoll, Ficoll, Nycodenz, Histodenz or sucrose gradients, are used to separate desired spore populations from other materials in the fecal material.

Also provided herein are methods of producing spore populations that combine two or more of the treatments described herein in order to synergistically purify the desired spores while killing or removing undesired materials and/or activities from the spore population. It is generally desirable to retain the spore populations under non-germinating and non-growth promoting conditions and media, in order to minimize the growth of pathogenic bacteria present in the spore populations and to minimize the germination of spores into vegetative bacterial cells.

Pharmaceutical Compositions and Formulations of the Invention

Formulations

Provided are formulations for administration to humans and other subjects in need thereof. Generally the bacterial compositions are combined with additional active and/or inactive materials in order to produce a final product, which may be in single dosage unit or in a multi-dose format.

In some embodiments, the composition comprises at least one carbohydrate. A “carbohydrate” refers to a sugar or polymer of sugars. The terms “saccharide,” “polysaccharide,” “carbohydrate,” and “oligosaccharide” may be used interchangeably. Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule. Carbohydrates generally have the molecular formula C_(n)H_(2n)O_(n). A carbohydrate can be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide. The most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose. Disaccharides are two joined monosaccharides. Exemplary disaccharides include sucrose, maltose, cellobiose, and lactose. Typically, an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, stachyose), and polysaccharides include six or more monosaccharide units. Exemplary polysaccharides include starch, glycogen, and cellulose. Carbohydrates can contain modified saccharide units, such as 2′-deoxyribose wherein a hydroxyl group is removed, 2′-fluororibose wherein a hydroxyl group is replace with a fluorine, or N-acetylglucosamine, a nitrogen-containing form of glucose (e.g., 2′-fluororibose, deoxyribose, and hexose). Carbohydrates can exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.

In some embodiments, the composition comprises at least one lipid. As used herein, a “lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans). In some embodiments, the lipid comprises at least one fatty acid selected from lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16:1), margaric acid (17:0), heptadecenoic acid (17:1), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid (20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoic acid (22:1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6) (DHA), and tetracosanoic acid (24:0). In other embodiments, the composition comprises at least one modified lipid, for example, a lipid that has been modified by cooking.

In some embodiments, the composition comprises at least one supplemental mineral or mineral source. Examples of minerals include, without limitation: chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium. Suitable forms of any of the foregoing minerals include soluble mineral salts, slightly soluble mineral salts, insoluble mineral salts, chelated minerals, mineral complexes, non-reactive minerals such as carbonyl minerals, and reduced minerals, and combinations thereof.

In certain embodiments, the composition comprises at least one supplemental vitamin. The at least one vitamin can be fat-soluble or water soluble vitamins. Suitable vitamins include but are not limited to vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin. Suitable forms of any of the foregoing are salts of the vitamin, derivatives of the vitamin, compounds having the same or similar activity of the vitamin, and metabolites of the vitamin.

In other embodiments, the composition comprises an excipient. Non-limiting examples of suitable excipients include a buffering agent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, and a coloring agent.

In another embodiment, the excipient is a buffering agent. Non-limiting examples of suitable buffering agents include sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate.

In some embodiments, the excipient comprises a preservative. Non-limiting examples of suitable preservatives include antioxidants, such as alpha-tocopherol and ascorbate, and antimicrobials, such as parabens, chlorobutanol, and phenol.

In other embodiments, the composition comprises a binder as an excipient. Non-limiting examples of suitable binders include starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C₁₂-C₁₈ fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, and combinations thereof.

In another embodiment, the composition comprises a lubricant as an excipient. Non-limiting examples of suitable lubricants include magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and light mineral oil.

In other embodiments, the composition comprises a dispersion enhancer as an excipient. Non-limiting examples of suitable dispersants include starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and microcrystalline cellulose as high HLB emulsifier surfactants.

In some embodiments, the composition comprises a disintegrant as an excipient. In other embodiments, the disintegrant is a non-effervescent disintegrant. Non-limiting examples of suitable non-effervescent disintegrants include starches such as corn starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, gums such as agar, guar, locust bean, karaya, pecitin, and tragacanth. In another embodiment, the disintegrant is an effervescent disintegrant. Non-limiting examples of suitable effervescent disintegrants include sodium bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid.

In another embodiment, the excipient comprises a flavoring agent. Flavoring agents can be chosen from synthetic flavor oils and flavoring aromatics; natural oils; extracts from plants, leaves, flowers, and fruits; and combinations thereof. In some embodiments the flavoring agent is selected from cinnamon oils; oil of wintergreen; peppermint oils; clover oil; hay oil; anise oil; eucalyptus; vanilla; citrus oil such as lemon oil, orange oil, grape and grapefruit oil; and fruit essences including apple, peach, pear, strawberry, raspberry, cherry, plum, pineapple, and apricot.

In other embodiments, the excipient comprises a sweetener. Non-limiting examples of suitable sweeteners include glucose (corn syrup), dextrose, invert sugar, fructose, and mixtures thereof (when not used as a carrier); saccharin and its various salts such as the sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia Rebaudiana (Stevioside); chloro derivatives of sucrose such as sucralose; and sugar alcohols such as sorbitol, mannitol, sylitol, and the like. Also contemplated are hydrogenated starch hydrolysates and the synthetic sweetener 3,6-dihydro-6-methyl-1,2,3-oxathiazin-4-one-2,2-dioxide, particularly the potassium salt (acesulfame-K), and sodium and calcium salts thereof.

In yet other embodiments, the composition comprises a coloring agent. Non-limiting examples of suitable color agents include food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), and external drug and cosmetic colors (Ext. D&C). The coloring agents can be used as dyes or their corresponding lakes.

The weight fraction of the excipient or combination of excipients in the formulation is usually about 99% or less, such as about 95% or less, about 90% or less, about 85% or less, about 80% or less, about 75% or less, about 70% or less, about 65% or less, about 60% or less, about 55% or less, 50% or less, about 45% or less, about 40% or less, about 35% or less, about 30% or less, about 25% or less, about 20% or less, about 15% or less, about 10% or less, about 5% or less, about 2% or less, or about 1% or less of the total weight of the composition.

The bacterial compositions disclosed herein can be formulated into a variety of forms and administered by a number of different means. The compositions can be administered orally, rectally, or parenterally, in formulations containing conventionally acceptable carriers, adjuvants, and vehicles as desired. The term “parenteral” as used herein includes subcutaneous, intravenous, intramuscular, or intrasternal injection and infusion techniques. In an exemplary embodiment, the bacterial composition is administered orally.

Solid dosage forms for oral administration include capsules, tablets, caplets, pills, troches, lozenges, powders, and granules. A capsule typically comprises a core material comprising a bacterial composition and a shell wall that encapsulates the core material. In some embodiments, the core material comprises at least one of a solid, a liquid, and an emulsion. In other embodiments, the shell wall material comprises at least one of a soft gelatin, a hard gelatin, and a polymer. Suitable polymers include, but are not limited to: cellulosic polymers such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose (HPMC), methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and copolymers, such as those formed from acrylic acid, methacrylic acid, methyl acrylate, ammonio methylacrylate, ethyl acrylate, methyl methacrylate and/or ethyl methacrylate (e.g., those copolymers sold under the trade name “Eudragit”); vinyl polymers and copolymers such as polyvinyl pyrrolidone, polyvinyl acetate, polyvinylacetate phthalate, vinylacetate crotonic acid copolymer, and ethylene-vinyl acetate copolymers; and shellac (purified lac). In yet other embodiments, at least one polymer functions as taste-masking agents.

Tablets, pills, and the like can be compressed, multiply compressed, multiply layered, and/or coated. The coating can be single or multiple. In one embodiment, the coating material comprises at least one of a saccharide, a polysaccharide, and glycoproteins extracted from at least one of a plant, a fungus, and a microbe. Non-limiting examples include corn starch, wheat starch, potato starch, tapioca starch, cellulose, hemicellulose, dextrans, maltodextrin, cyclodextrins, inulins, pectin, mannans, gum arabic, locust bean gum, mesquite gum, guar gum, gum karaya, gum ghatti, tragacanth gum, funori, carrageenans, agar, alginates, chitosans, or gellan gum. In some embodiments the coating material comprises a protein. In another embodiment, the coating material comprises at least one of a fat and an oil. In other embodiments, the at least one of a fat and an oil is high temperature melting. In yet another embodiment, the at least one of a fat and an oil is hydrogenated or partially hydrogenated. In one embodiment, the at least one of a fat and an oil is derived from a plant. In other embodiments, the at least one of a fat and an oil comprises at least one of glycerides, free fatty acids, and fatty acid esters. In some embodiments, the coating material comprises at least one edible wax. The edible wax can be derived from animals, insects, or plants. Non-limiting examples include beeswax, lanolin, bayberry wax, carnauba wax, and rice bran wax. Tablets and pills can additionally be prepared with enteric coatings.

Alternatively, powders or granules embodying the bacterial compositions disclosed herein can be incorporated into a food product. In some embodiments, the food product is a drink for oral administration. Non-limiting examples of a suitable drink include fruit juice, a fruit drink, an artificially flavored drink, an artificially sweetened drink, a carbonated beverage, a sports drink, a liquid diary product, a shake, an alcoholic beverage, a caffeinated beverage, infant formula and so forth. Other suitable means for oral administration include aqueous and nonaqueous solutions, emulsions, suspensions and solutions and/or suspensions reconstituted from non-effervescent granules, containing at least one of suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, coloring agents, and flavoring agents.

In some embodiments, the food product can be a solid foodstuff. Suitable examples of a solid foodstuff include without limitation a food bar, a snack bar, a cookie, a brownie, a muffin, a cracker, an ice cream bar, a frozen yogurt bar, and the like.

In other embodiments, the compositions disclosed herein are incorporated into a therapeutic food. In some embodiments, the therapeutic food is a ready-to-use food that optionally contains some or all essential macronutrients and micronutrients. In another embodiment, the compositions disclosed herein are incorporated into a supplementary food that is designed to be blended into an existing meal. In one embodiment, the supplemental food contains some or all essential macronutrients and micronutrients. In another embodiment, the bacterial compositions disclosed herein are blended with or added to an existing food to fortify the food's protein nutrition. Examples include food staples (grain, salt, sugar, cooking oil, margarine), beverages (coffee, tea, soda, beer, liquor, sports drinks), snacks, sweets and other foods.

In one embodiment, the formulations are filled into gelatin capsules for oral administration. An example of an appropriate capsule is a 250 mg gelatin capsule containing from 10 (up to 100 mg) of lyophilized powder (10⁸ to 10¹¹ bacteria), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate. In an alternative embodiment, from 10⁵ to 10¹² bacteria may be used, 10⁵ to 10⁷, 10⁶ to 10⁷, or 10⁸ to 10¹⁰, with attendant adjustments of the excipients if necessary. In an alternative embodiment, an enteric-coated capsule or tablet or with a buffering or protective composition can be used.

EXAMPLES

Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.

The practice of the present invention will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T. E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); A. L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pa.: Mack Publishing Company, 1990); Carey and Sundberg Advanced Organic Chemistry 3^(rd) Ed. (Plenum Press) Vols A and B(1992).

Example 1: Sequence-based Genomic Characterization of Operational Taxonomic Units (OTU) and Functional Genes

Method for Determining 16S rDNA Gene Sequence

As described above, OTUs are defined either by full 16S sequencing of the rRNA gene, by sequencing of a specific hypervariable region of this gene (i.e. V1, V2, V3, V4, V5, V6, V7, V8, or V9), or by sequencing of any combination of hypervariable regions from this gene (e.g. V1-3 or V3-5). The bacterial 16S rRNA gene is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most microbes. rRNA gene sequencing methods are applicable to both the analysis of non-enriched samples, but also for identification of microbes after enrichment steps that either enrich the microbes of interest from the microbial composition and/or the nucleic acids that harbor the appropriate rDNA gene sequences as described below. For example, enrichment treatments prior to 16S rDNA gene characterization will increase the sensitivity of 16S as well as other molecular-based characterization nucleic acid purified from the microbes.

Using well known techniques, in order to determine the full 16S sequence or the sequence of any hypervariable region of the 16S rRNA sequence, genomic DNA is extracted from a bacterial sample, the 16S rDNA (full region or specific hypervariable regions) amplified using polymerase chain reaction (PCR), the PCR products cleaned, and nucleotide sequences delineated to determine the genetic composition of 16S gene or subdomain of the gene. If full 16S sequencing is performed, the sequencing method used may be, but is not limited to, Sanger sequencing. If one or more hypervariable regions are used, such as the V4 region, the sequencing may be, but is not limited to being, performed using the Sanger method or using a next-generation sequencing method, such as an Illumina (sequencing by synthesis) method using barcoded primers allowing for multiplex reactions.

Method for Determining 18S rDNA and ITS Gene Sequence

Methods to assign and identify fungal OTUs by genetic means can be accomplished by analyzing 18S sequences and the internal transcribed spacer (ITS). The rRNA of fungi that forms the core of the ribosome is transcribed as a signal gene and consists of the 8S, 5.8S and 28S regions with ITS4 and 5 between the 8S and 5.8S and 5.8S and 28S regions, respectively. These two intercistronic segments between the 18S and 5.8S and 5.8S and 28S regions are removed by splicing and contain significant variation between species for barcoding purposes as previously described (Schoch et al Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109:6241-6246. 2012). 18S rDNA is traditionally used for phylogenetic reconstruction however the ITS can serve this function as it is generally highly conserved but contains hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most fungus.

Using well known techniques, in order to determine the full 18S and ITS sequences or a smaller hypervariable section of these sequences, genomic DNA is extracted from a microbial sample, the rDNA amplified using polymerase chain reaction (PCR), the PCR products cleaned, and nucleotide sequences delineated to determine the genetic composition rDNA gene or subdomain of the gene. The sequencing method used may be, but is not limited to, Sanger sequencing or using a next-generation sequencing method, such as an Illumina (sequencing by synthesis) method using barcoded primers allowing for multiplex reactions.

Method for Determining Other Marker Gene Sequences

In addition to the 16S and 18S rRNA gene, one may define an OTU by sequencing a selected set of genes that are known to be marker genes for a given species or taxonomic group of OTUs. These genes may alternatively be assayed using a PCR-based screening strategy. As example, various strains of pathogenic Escherichia coli can be distinguished using DNAs from the genes that encode heat-labile (LTI, LTIIa, and LTIIb) and heat-stable (STI and STII) toxins, verotoxin types 1, 2, and 2e (VT1, VT2, and VT2e, respectively), cytotoxic necrotizing factors (CNF1 and CNF2), attaching and effacing mechanisms (eaeA), enteroaggregative mechanisms (Eagg), and enteroinvasive mechanisms (Einv). The optimal genes to utilize for taxonomic assignment of OTUs by use of marker genes will be familiar to one with ordinary skill of the art of sequence based taxonomic identification.

Genomic DNA Extraction

Genomic DNA is extracted from pure microbial cultures using a hot alkaline lysis method. 1 μl of microbial culture is added to 9 μl of Lysis Buffer (25 mM NaOH, 0.2 mM EDTA) and the mixture is incubated at 95° C. for 30 minutes. Subsequently, the samples are cooled to 4° C. and neutralized by the addition of 10 μl of Neutralization Buffer (40 mM Tris-HCl) and then diluted 10-fold in Elution Buffer (10 mM Tris-HCl). Alternatively, genomic DNA is extracted from pure microbial cultures using commercially available kits such as the Mo Bio Ultraclean® Microbial DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.) or by standard methods known to those skilled in the art. For fungal samples, DNA extraction can be performed by methods described previously (US20120135127) for producing lysates from fungal fruiting bodies by mechanical grinding methods.

Amplification of 16S Sequences for Downstream Sanger Sequencing

To amplify bacterial 16S rDNA (e.g, in FIG. 1), 2 μl of extracted gDNA is added to a 20 μl final volume PCR reaction. For full-length 16 sequencing the PCR reaction also contains 1× HotMasterMix (5PRIME, Gaithersburg, Md.), 250 nM of 27f (AGRGTTTGATCMTGGCTCAG (SEQ ID NO: 2033), IDT, Coralville, Iowa), and 250 nM of 1492r (TACGGYTACCTTGTTAYGACTT (SEQ ID NO: 2034), IDT, Coralville, Iowa), with PCR Water (Mo Bio Laboratories, Carlsbad, Calif.) for the balance of the volume.

FIG. 1 shows the hypervariable regions mapped onto a 16s sequence and the sequence regions corresponding to these sequences on a sequence map. A schematic is shown of a 16S rRNA gene and the figure denotes the coordinates of hypervariable regions 1-9 (V1-V9), according to an embodiment of the invention. Coordinates of V1-V9 are 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294, and 1435-1465 respectively, based on numbering using E. coli system of nomenclature defined by Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene (16S rRNA) from Escherichia coli, PNAS 75(10):4801-4805 (1978).

Alternatively, other universal bacterial primers or thermostable polymerases known to those skilled in the art are used. For example, primers are available to those skilled in the art for the sequencing of the the “V1-V9 regions” of the 16S rRNA (e.g., FIG. 1). These regions refer to the first through ninth hypervariable regions of the 16S rRNA gene that are used for genetic typing of bacterial samples. These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. See Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805 (1978). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU. A person of ordinary skill in the art can identify the specific hypervariable regions of a candidate 16S rRNA (e.g., FIG. 1) by comparing the candidate sequence in question to the reference sequence (as in FIG. 2) and identifying the hypervariable regions based on similarity to the reference hypervariable regions. FIG. 2 highlights in bold the nucleotide sequences for each hypervariable region in the exemplary reference E. coli 16S sequence described by Brosius et al.

The PCR is performed on commercially available thermocyclers such as a BioRad MyCycler™ Thermal Cycler (BioRad, Hercules, Calif.). The reactions are run at 94° C. for 2 minutes followed by 30 cycles of 94° C. for 30 seconds, 51° C. for 30 seconds, and 68° C. for 1 minute 30 seconds, followed by a 7 minute extension at 72° C. and an indefinite hold at 4° C. Following PCR, gel electrophoresis of a portion of the reaction products is used to confirm successful amplification of a ˜1.5 kb product.

To remove nucleotides and oligonucleotides from the PCR products, 2 μl of HT ExoSap-IT (Affymetrix, Santa Clara, Calif.) is added to 5 μl of PCR product followed by a 15 minute incubation at 37° C. and then a 15 minute inactivation at 80° C.

Amplification of 16S Sequences for Downstream Characterization By Massively Parallel Sequencing Technologies

Amplification performed for downstream sequencing by short read technologies such as Illumina require amplification using primers known to those skilled in the art that additionally include a sequence-based barcoded tag. As example, to amplify the 16s hypervariable region V4 region of bacterial 16S rDNA, 2 μl of extracted gDNA is added to a 20 μl final volume PCR reaction. The PCR reaction also contains 1× HotMasterMix (5PRIME, Gaithersburg, Md.), 200 nM of V4_515f_adapt (AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGTGTGCCAGCMGCCGCGG TAA (SEQ ID NO: 2035), IDT, Coralville, Iowa), and 200 nM of barcoded 806rbc (CAAGCAGAAGACGGCATACGAGAT_12bpGolayBarcode_AGTCAGTCAGCCGGACTAC HVGGGTWTCTAAT (SEQ ID NOs: 2036-2037, respectively, in order of appearance), IDT, Coralville, Iowa), with PCR Water (Mo Bio Laboratories, Carlsbad, Calif.) for the balance of the volume. These primers incorporate barcoded adapters for Illumina sequencing by synthesis. Optionally, identical replicate, triplicate, or quadruplicate reactions may be performed. Alternatively other universal bacterial primers or thermostable polymerases known to those skilled in the art are used to obtain different amplification and sequencing error rates as well as results on alternative sequencing technologies.

The PCR amplification is performed on commercially available thermocyclers such as a BioRad MyCycler™ Thermal Cycler (BioRad, Hercules, Calif.). The reactions are run at 94° C. for 3 minutes followed by 25 cycles of 94° C. for 45 seconds, 50° C. for 1 minute, and 72° C. for 1 minute 30 seconds, followed by a 10 minute extension at 72° C. and a indefinite hold at 4° C. Following PCR, gel electrophoresis of a portion of the reaction products is used to confirm successful amplification of a ˜1.5 kb product. PCR cleanup is performed as described above.

Sanger Sequencing of Target Amplicons from Pure Homogeneous Samples

To detect nucleic acids for each sample, two sequencing reactions are performed to generate a forward and reverse sequencing read. For full-length 16s sequencing primers 27f and 1492r are used. 40 ng of ExoSap-IT-cleaned PCR products are mixed with 25 pmol of sequencing primer and Mo Bio Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) to 15 μl total volume. This reaction is submitted to a commercial sequencing organization such as Genewiz (South Plainfield, N.J.) for Sanger sequencing.

Amplification of 18S and ITS regions for Downstream Sequencing

To amplify the 18S or ITS regions, 2 μL fungal DNA were amplified in a final volume of 30 μL with 15 μL AmpliTaq Gold 360 Mastermix, PCR primers, and water. The forward and reverse primers for PCR of the ITS region are 5′-TCCTCCGCTTATTGATATGC-3′ (SEQ ID NO: 2038) and 5′-GGAAGTAAAAGTCGTAACAAGG-3′ (SEQ ID NO: 2039) and are added at 0.2 uM concentration each. The forward and reverse primers for the 18s region are 5′-GTAGTCATATGCTTGTCTC-3′ (SEQ ID NO: 2040) and 5′-CTTCCGTCAATTCCTTTAAG-3′ (SEQ ID NO: 2041) and are added at 0.4 uM concentration each. PCR is performed with the following protocol: 95 C for 10 min, 35 cycles of 95 C for 15 seconds, 52 C for 30 seconds, 72 C for 1.5 s; and finally 72 C for 7 minutes followed by storage at 4 C. All forward primers contained the M13F-20 sequencing primer, and reverse primers included the M13R-27 sequencing primer. PCR products (3 μL) were enzymatically cleaned before cycle sequencing with 1 μL ExoSap-IT and 1 μL Tris EDTA and incubated at 37° C. for 20 min followed by 80° C. for 15 min. Cycle sequencing reactions contained 5 μL cleaned PCR product, 2 μL BigDye Terminator v3.1 Ready Reaction Mix, 1 μL 5× Sequencing Buffer, 1.6 pmol of appropriate sequencing primers designed by one skilled in the art, and water in a final volume of 10 μL. The standard cycle sequencing protocol is 27 cycles of 10 s at 96° C., 5 s at 50° C., 4 min at 60° C., and hold at 4° C. Sequencing cleaning is performed with the BigDye XTerminator Purification Kit as recommended by the manufacturer for 10-μL volumes. The genetic sequence of the resulting 18S and ITS sequences is performed using methods familiar to one with ordinary skill in the art using either Sanger sequencing technology or next-generation sequencing technologies such as but not limited to Illumina.

Preparation of Extracted Nucleic Acids for Metagenomic Characterization by Massively Parallel Sequencing Technologies

Extracted nucleic acids (DNA or RNA) are purified and prepared by downstream sequencing using standard methods familiar to one with ordinary skill in the art and as described by the sequencing technology's manufactures instructions for library preparation. In short, RNA or DNA are purified using standard purification kits such as but not limited to Qiagen's RNeasy Kit or Promega's Genomic DNA purification kit. For RNA, the RNA is converted to cDNA prior to sequence library construction. Following purification of nucleic acids, RNA is converted to cDNA using reverse transcription technology such as but not limited to Nugen Ovation RNA-Seq System or Illumina Truseq as per the manufacturer's instructions. Extracted DNA or transcribed cDNA are sheared using physical (e.g., Hydroshear), acoustic (e.g., Covaris), or molecular (e.g., Nextera) technologies and then size selected as per the sequencing technologies manufacturer's recommendations. Following size selection, nucleic acids are prepared for sequencing as per the manufacturer's instructions for sample indexing and sequencing adapter ligation using methods familiar to one with ordinary skill in the art of genomic sequencing.

Massively Parallel Sequencing of Target Amplicons from Heterogeneous Samples DNA Quantification & Library Construction

The cleaned PCR amplification products are quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies, Grand Island, N.Y.) according to the manufacturer's instructions. Following quantification, the barcoded cleaned PCR products are combined such that each distinct PCR product is at an equimolar ratio to create a prepared Illumina library.

Nucleic Acid Detection

The prepared library is sequenced on Illumina HiSeq or MiSeq sequencers (Illumina, San Diego, Calif.) with cluster generation, template hybridization, isothermal amplification, linearization, blocking and denaturation and hybridization of the sequencing primers performed according to the manufacturer's instructions. 16SV4SeqFw (TATGGTAATTGTGTGCCAGCMGCCGCGGTAA (SEQ ID NO: 2042)), 16SV4SeqRev (AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT (SEQ ID NO. 2037)), and 16SV4Index (ATTAGAWACCCBDGTAGTCCGGCTGACTGACT (SEQ ID NO: 2043) (IDT, Coralville, Iowa) are used for sequencing. Other sequencing technologies can be used such as but not limited to 454, Pacific Biosciences, Helicos, Ion Torrent, and Nanopore using protocols that are standard to someone skilled in the art of genomic sequencing.

Example 2. Sequence Read Annotation

Primary Read Annotation

Nucleic acid sequences are analyzed and annotated to define taxonomic assignments using sequence similarity and phylogenetic placement methods or a combination of the two strategies. A similar approach can be used to annotate protein names, protein function, transcription factor names, and any other classification schema for nucleic acid sequences. Sequence similarity based methods include those familiar to individuals skilled in the art including, but not limited to BLAST, BLASTx, tBLASTn, tBLASTx, RDP-classifier, DNAclust, and various implementations of these algorithms such as Qiime or Mothur. These methods rely on mapping a sequence read to a reference database and selecting the match with the best score and e-value. Common databases include, but are not limited to the Human Microbiome Project, NCBI non-redundant database, Greengenes, RDP, and Silva for taxonomic assignments. For functional assignments reads are mapped to various functional databases such as but not limited to COG, KEGG, BioCyc, and MetaCyc. Further functional annotations can be derived from 16S taxonomic annotations using programs such as PICRUST (M. Langille, et al 2013. Nature Biotechnology 31, 814-821). Phylogenetic methods can be used in combination with sequence similarity methods to improve the calling accuracy of an annotation or taxonomic assignment. Here tree topologies and nodal structure are used to refine the resolution of the analysis. In this approach we analyze nucleic acid sequences using one of numerous sequence similarity approaches and leverage phylogenetic methods that are well known to those skilled in the art, including but not limited to maximum likelihood phylogenetic reconstruction (see e.g. Liu K, Linder C R, and Warnow T. 2011. RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation. PLoS ONE 6: e27731. McGuire G, Denham M C, and Balding D J. 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol 18: 481-490. Wróbel B. 2008. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J. Appl. Genet. 49: 49-67.) Sequence reads (e.g. 16S, 18S, or ITS) are placed into a reference phylogeny comprised of appropriate reference sequences. Annotations are made based on the placement of the read in the phylogenetic tree. The certainty or significance of the OTU annotation is defined based on the OTU's sequence similarity to a reference nucleic acid sequence and the proximity of the OTU sequence relative to one or more reference sequences in the phylogeny. As an example, the specificity of a taxonomic assignment is defined with confidence at the the level of Family, Genus, Species, or Strain with the confidence determined based on the position of bootstrap supported branches in the reference phylogenetic tree relative to the placement of the OTU sequence being interrogated. Nucleic acid sequences can be assigned functional annotations using the methods described above.

Clade Assignments

The ability of 16S-V4 OTU identification to assign an OTU as a specific species depends in part on the resolving power of the 16S-V4 region of the 16S gene for a particular species or group of species. Both the density of available reference 16S sequences for different regions of the tree as well as the inherent variability in the 16S gene between different species will determine the definitiveness of a taxonomic annotation. Given the topological nature of a phylogenetic tree and the fact that tree represents hierarchical relationships of OTUs to one another based on their sequence similarity and an underlying evolutionary model, taxonomic annotations of a read can be rolled up to a higher level using a clade-based assignment procedure. Using this approach, clades are defined based on the topology of a phylogenetic tree that is constructed from full-length 16S sequences using maximum likelihood or other phylogenetic models familiar to individuals with ordinary skill in the art of phylogenetics. Clades are constructed to ensure that all OTUs in a given clade are: (i) within a specified number of bootstrap supported nodes from one another (generally, 1-5 bootstraps), and (ii) share a defined percent similarity (for 16S molecular data typically set to 95%-97% sequence similarity). OTUs that are within the same clade can be distinguished as genetically and phylogenetically distinct from OTUs in a different clade based on 16S-V4 sequence data. OTUs falling within the same clade are evolutionarily closely related and may or may not be distinguishable from one another using 16S-V4 sequence data. The power of clade based analysis is that members of the same clade, due to their evolutionary relatedness, are likely to play similar functional roles in a microbial ecology such as that found in the human gut. Compositions substituting one species with another from the same clade are likely to have conserved ecological function and therefore are useful in the present invention. Notably in addition to 16S-V4 sequences, clade-based analysis can be used to analyze 18S, ITS, and other genetic sequences.

Notably, 16S sequences of isolates of a given OTU are phylogenetically placed within their respective clades, sometimes in conflict with the microbiological-based assignment of species and genus that may have preceded 16S-based assignment. Discrepancies between taxonomic assignment based on microbiological characteristics versus genetic sequencing are known to exist from the literature.

For a given network ecology or functional network ecology one can define a set of OTUs from the network's representative clades. As example, if a network was comprised of clade_100 and clade_102 it can be said to be comprised of at least one OTU from the group consisting of Corynebacterium coyleae, Corynebacterium mucifaciens, and Corynebacterium ureicelerivorans, and at least one OTU from the group consisting of Corynebacterium appendicis, Corynebacterium genitalium, Corynebacterium glaucum, Corynebacterium imitans, Corynebacterium riegelii, Corynebacterium sp. L_2012475, Corynebacterium sp. NML 93_0481, Corynebacterium sundsvallense, and Corynebacterium tuscaniae (see Table 1). Conversely as example, if a network was said to consist of Corynebacterium coyleae and/or Corynebacterium mucifaciens and/or Corynebacterium ureicelerivorans, and also consisted of Corynebacterium appendicis and/or Corynebacterium genitalium and/or Corynebacterium glaucum and/or Corynebacterium imitans and/or Corynebacterium riegelii and/or Corynebacterium sp. L_2012475 and/or Corynebacterium sp. NML 93_0481 and/or Corynebacterium sundsvallense and/or Corynebacterium tuscaniae it can be said to be comprised of clade_100 and clade_102.

The applicants made clade assignments to all OTUs reported in the application using the above described method and these assignments are reported in Table 1. In some embodiments, the network analysis permits substitutions of clade_172 by clade_172i. In another embodiment, the network analysis permits substitutions of clade_198 by clade_198i. In another embodiment, the network analysis permits substitutions of clade_260 by clade_260c, clade_260g or clade_260h. In another embodiment, the network analysis permits substitutions of clade_262 by clade_262i. In another embodiment, the network analysis permits substitutions of clade_309 by clade_309c, clade_309e, clade_309g, clade_309h or clade_309i. In another embodiment, the network analysis permits substitutions of clade_313 by clade_313f. In another embodiment, the network analysis permits substitutions of clade_325 by clade_325f. In another embodiment, the network analysis permits substitutions of clade_335 by clade_335i. In another embodiment, the network analysis permits substitutions of clade_351 by clade_351e. In another embodiment, the network analysis permits substitutions of clade_354 by clade_354e. In another embodiment, the network analysis permits substitutions of clade_360 by clade_360c, clade_360g, clade_360h, or clade_360i. In another embodiment, the network analysis permits substitutions of clade_378 by clade_378e. In another embodiment, the network analysis permits substitutions of clade_38 by clade_38e or clade_38i. In another embodiment, the network analysis permits substitutions of clade_408 by clade_408b, clade_408d, clade_408f, clade_408g or clade_408h. In another embodiment, the network analysis permits substitutions of clade_420 by clade_420f. In another embodiment, the network analysis permits substitutions of clade_444 by clade_444i. In another embodiment, the network analysis permits substitutions of clade_478 by clade_478i. In another embodiment, the network analysis permits substitutions of clade_479 by clade_479c, by clade_479g or by clade_479h. In another embodiment, the network analysis permits substitutions of clade_481 by clade_481a, clade_481b, clade_481e, clade_481g, clade_481h or by clade_481i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_497 by clade_497e or by clade_497f. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_512 by clade_512i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_516 by clade_516c, by clade_516g or by clade_516h. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_522 by clade_522i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_553 by clade_553i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_566 by clade_566f. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_572 by clade_572i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_65 by clade_65e. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_92 by clade_92e or by clade_92i. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_96 by clade_96g or by clade_96h. In another embodiment, the network analysis permits the network analysis permits substitutions of clade_98 by clade_98i. These permitted clade substitutions are described in Table 22.

Metagenomic Read Annotation

Metagenomic or whole genome shotgun sequence data is annotated as described above, with the additional step that sequences are either clustered or assembled prior to annotation. Following sequence characterization as described above, sequence reads are demultiplexed using the indexing (i.e. barcodes). Following demultiplexing sequence reads are either: (i) clustered using a rapid clustering algorithm such as but not limited to UCLUST (http://drive5.com/usearch/manual/uclust algo.html) or hash methods such VICUNA (Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J. Lennon, Joshua Z. Levin, James Qu, Elizabeth M. Ryan, Michael C. Zody, and Matthew R. Henn. 2012. De novo assembly of highly diverse viral populations. BMC Genomics 13:475). Following clustering a representative read for each cluster is identified based and analyzed as described above in “Primary Read Annotation”. The result of the primary annotation is then applied to all reads in a given cluster. (ii) A second strategy for metagenomic sequence analysis is genome assembly followed by annotation of genomic assemblies using a platform such as but not limited to MetAMOS (T J. Treangen et al. 2013 Geneome Biology 14:R2), HUMAaN (Abubucker S, Segata N, Goll J, Schubert A M, Izard J, Cantarel B L, Rodriguez-Mueller B, Zucker J, Thiagaraj an M, Henrissat B, et al. 2012. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome ed. J. A. Eisen. PLoS Computational Biology 8: e1002358) and other methods familiar to one with ordinary skill in the art.

Example 3. OTU Identification Using Microbial Culturing Techniques

The identity of the bacterial species which grow up from a complex fraction can be determined in multiple ways. First, individual colonies are picked into liquid media in a 96 well format, grown up and saved as 15% glycerol stocks at −80° C. Aliquots of the cultures are placed into cell lysis buffer and colony PCR methods can be used to amplify and sequence the 16S rDNA gene (Example 1). Alternatively, colonies are streaked to purity in several passages on solid media. Well separated colonies are streaked onto the fresh plates of the same kind and incubated for 48-72 hours at 37° C. The process is repeated multiple times in order to ensure purity. Pure cultures are analyzed by phenotypic- or sequence-based methods, including 16S rDNA amplification and sequencing as described in Example 1. Sequence characterization of pure isolates or mixed communities e.g. plate scrapes and spore fractions can also include whole genome shotgun sequencing. The latter is valuable to determine the presence of genes associated with sporulation, antibiotic resistance, pathogenicity, and virulence. Colonies are also scraped from plates en masse and sequenced using a massively parallel sequencing method as described in Example 1, such that individual 16S signatures can be identified in a complex mixture. Optionally, the sample can be sequenced prior to germination (if appropriate DNA isolation procedures are used to lsye and release the DNA from spores) in order to compare the diversity of germinable species with the total number of species in a spore sample. As an alternative or complementary approach to 16S analysis, MALDI-TOF-mass spec is used for species identification (Barreau M, Pagnier I, La Scola B. 2013. Improving the identification of anaerobes in the clinical microbiology laboratory through MALDI-TOF mass spectrometry. Anaerobe 22: 123-125).

Example 4. Microbiological Strain Identification Approaches

Pure bacterial isolates are identified using microbiological methods as described in Wadsworth-KTL Anaerobic Microbiology Manual (Jouseimies-Somer H, Summanen P H, Citron D, Baron E, Wexler H M, Finegold S M. 2002. Wadsworth-KTL Anaerobic Bacteriology Manual), and The Manual of Clinical Microbiology (ASM Press, 10th Edition). These methods rely on phenotypes of strains and include Gram-staining to confirm Gram positive or negative staining behavior of the cell envelope, observance of colony morphologies on solid media, motility, cell morphology observed microscopically at 60× or 100× magnification including the presence of bacterial endospores and flagella. Biochemical tests that discriminate between genera and species are performed using appropriate selective and differential agars and/or commercially available kits for identification of Gram negative and Gram positive bacteria and yeast, for example, RapID tests (Remel) or API tests (bioMerieux). Similar identification tests can also be performed using instrumentation such as the Vitek 2 system (bioMerieux). Phenotypic tests that discriminate between genera and species and strains (for example the ability to use various carbon and nitrogen sources) can also be performed using growth and metabolic activity detection methods, for example the Biolog Microbial identification microplates. The profile of short chain fatty acid production during fermentation of particular carbon sources can also be used as a way to discriminate between species (Wadsworth-KTL Anaerobic Microbiology Manual, Jousimies-Somer, et al 2002). MALDI-TOF-mass spectrometry can also be used for species identification (as reviewed in Anaerobe 22:123).

Example 5. Computational Prediction of Network Ecologies

Source data comprising a genomic-based characterization of a microbiome of individual samples were used as input computationally delineate network ecologies that would have biological properties that are characteristic of a state of health and could catalzye a shift from a state of microbial dysbiosis to a state of health. Applicants obtained 16S and metagenomic sequence datasets from public data repositories (see e.g. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214. Data accessible at URL: hmpdacc.org) and MetaHit Project (Arumugam M, Raes J, Pelletier E, Paslier D L, Yamada T, Mende D R, Fernandes G R, Tap J, Bruls T, Batto J-M, et al. 2011. Enterotypes of the human gut microbiome. Nature 473: 174-180. Data accessible at URL: metahit.eu) for relevant microbiome studies in multiple disease indications including CDAD, Type 2 Diabetes, Ulcerative Colitis, and Irritable Bowel Disease, or generated data sets from samples directly using the methods described in Examples 1 & 2 and further described in the literature (see e.g. Aagaard K, Riehle K, Ma J, Segata N, Mistretta T-A, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, et al. 2012. A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy ed. A. J. Ratner. PLoS ONE 7: e36466. Jumpstart Consortium Human Microbiome Project Data Generation Working Group. 2012. Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research ed. J. Ravel. PLoS ONE 7: e39315. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.). Nucleic acid sequences were analyzed and taxonomic and phylogenetic assignments of specific OTUs were made using sequence similarity and phylogenetic methods that are well known to those skilled in the art, including but not limited to maximum likelihood phylogenetic reconstruction (see e.g. Liu K, Linder C R, and Warnow T. 2011. RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation. PLoS ONE 6: e27731. McGuire G, Denham M C, and Balding D J. 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol 18: 481-490. Wróbel B. 2008. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J. Appl. Genet. 49: 49-67.) From these taxonomic assignments OTUs and clades in the dataset were defined using the method described in Examples 1 and 2. The certainty of the OTU call was defined based on the OTU's sequence similarity to a reference nucleic acid sequence and the proximity of the OTU sequence relative to one or more reference sequences in the phylogeny. The specificity of an OTU's taxonomic and phlylogenetic assignment determines whether the match is assigned at the level of Family, Genus, Species, or Strain, and the confidence of this assignment is determined based on the position of bootstrap supported branches in the reference phylogenetic tree relative to the placement of the OTU sequence being interrogated. In addition, microbial OTU assignments may be obtained from assignments made in peer-reviewed publications.

Applicants designated individual subject samples to biologically relevant sample phenotypes such as but not limited to “healthy state,” “recurrent Clostridium difficile infection,” “Crohn's disease,” “Insulin Resistance,” “Obesity,” “Type 2 diabetes,” “Ulcerative Colitis”. In one embodiment samples are assigned to “health” and “disease” phenotypes. In another embodiment, samples are assigned higher resolution phenotype such as but not limited to: “health:human”, “health:mouse”, “health:human microbiome project”, “health:microbiota donor”, “health:microbiota recipient”, “disease:microbiota recipient”, or “disease:no treatment”, “disease:human”, or “disease:mouse”. In another embodiment, samples where assigned to higher resolution phenotypes, such as but not limited to those defined in FIG. 19 that characterize phenotypes specific to samples from fecal donors and patients who received a fecal microbial transplant from these donors. FIG. 19 shows phenotypes assigned to samples for the computational derivation of Network Ecologies that typify microbiome states of health (Hpost, Hdon, & Hgen) and states of disease (DdonF & DpreF).

In another embodiment, other phenotypes that define a category of disease or health that represents the underlying state of the population under study can be used. Applicants then computationally determined the microbial network ecologies for each phenotype using the OTU and clade assignments that comprise the microbial profile for each sample and the algorithms described above in the Section entitled “Method of Determining Network Ecologies.”

Tables 8, 11, and 14a below provide exemplary network ecologies that define states of health as compared to states of dysbiosis or disease for multiple disease indications. The disease indications for which the network ecologies represent a health state are denoted in Table 8, and Keystone and Non-Keystone OTUs (see Example 6) are delineated in Tables 9-10. Importantly, Network Ecologies that represent a state of health in one disease indication can represent states of health in additional disease states. Additionally, Keystone OTUs found in a network associated with health for different disease indications can overlap. Applicants found that a large number of network ecologies overlapped particularly between those associated with health in the cases of CDAD and Type 2 Diabetes despite the analysis of substantially different genomic data sets for the two diseases.

Example 6. Identification of Network Classes, Keystone OTUs, Clades, and Functional Modalities

Identification of Keystone OTUs, Clades and Functions

The human body is an ecosystem in which the microbiota and the microbiome play a significant role in the basic healthy function of human systems (e.g. metabolic, immunological, and neurological). The microbiota and resulting microbiome comprise an ecology of microorganisms that co-exist within single subjects interacting with one another and their host (i.e., the mammalian subject) to form a dynamic unit with inherent biodiversity and functional characteristics. Within these networks of interacting microbes (i.e. ecologies), particular members can contribute more significantly than others; as such these members are also found in many different ecologies, and the loss of these microbes from the ecology can have a significant impact on the functional capabilities of the specific ecology. Robert Paine coined the concept “Keystone Species” in 1969 (see Paine R T. 1969. A note on trophic complexity and community stability. The American Naturalist 103: 91-93) to describe the existence of such lynchpin species that are integral to a given ecosystem regardless of their abundance in the ecological community. Paine originally describe the role of the starfish Pisaster ochraceus in marine systems and since the concept has been experimentally validated in numerous ecosystems.

Keystone OTUs (as shown in Table 9), Phylogenetic Clades (a.k.a. Clades), and/or Functions (for example, but not limited to, KEGG Orthology Pathways) are computationally-derived by analysis of network ecologies elucidated from a defined set of samples that share a specific phenotype. Keystone OTUs, Clades and/or Functions are defined as all Nodes within a defined set of networks that meet two or more of the following criteria. Using Criterion 1, the node is frequently observed in networks, and the networks in which the node is observed are found in a large number of individual subjects; the frequency of occurrence of these Nodes in networks and the pervasiveness of the networks in individuals indicates these Nodes perform an important biological function in many individuals. Using Criterion 2, the node is frequently observed in networks, and the Node is observed contains a large number of edges connecting it to other nodes in the network. These Nodes are thus “super-connectors”, meaning that they form a nucleus of a majority of networks (See FIG. 17) and as such have high biological significance with respect to their functional contributions to a given ecology.

FIG. 17 is a schematic representation of how Keystone OTUs (nodes 2 and 4, shaded circles) are central members of many network ecologies that contain non-Keystone OTUs (nodes 1, 3, and 5-9). Distinct network ecologies include [node 2--node 7], [node--3--node 2--node--4], [node 2--node 4--node 5--node 6--node 7], [node 1--node 2--node 8--node 9], and [node--node 3].

Using Criterion 3, the Node is found in networks containing a large number of Nodes (i.e., they are large networks), and the networks in which the Node is found occur in a large number of subjects; these networks are potentially of high interest as it is unlikely that large networks occurring in many individuals would occur by chance alone strongly suggesting biological relevance. Optionally, the required thresholds for the frequency at which a Node is observed in network ecologies, the frequency at which a given network is observed across subject samples, and the size of a given network to be considered a Keystone Node are defined by the 50th, 70th, 80th, or 90th percentiles of the distribution of these variables. Optionally, the required thresholds are defined by the value for a given variable that is significantly different from the mean or median value for a given variable using standard parametric or non-parametric measures of statistical significance. In another embodiment a Keystone Node is defined as one that occurs in a sample phenotype of interest such as but not limited to “health” and simultaneously does not occur in a sample phenotype that is not of interest such as but not limited to “disease.” Optionally, a Keystone Node is defined as one that is shown to be significantly different from what is observed using permuted test datasets to measure significance. In another embodiment of Criterion 2 Keystone OTUs, Clades, or Functions can be defined using a hierarchical clustering method that clusters Networks based on their OTU, Clade, or functional pathways. Statistically significant branch points in the hierarchy are defined based on the topological overlap measure; this measure is a highly robust measure of network interconnectedness (Langfelder P, Zhang B, Horvath S. 2008. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24: 719-720.). Once these branch points are defined the Keystones are delineated as OTUs, clades or functional pathways that are found consistently across all networks in all or a subset of the network clusters.

Applicants defined the Keystone OTUs and Clades characteristic of health states for the computationally determined networks reported in Table 8 for the various disease indications analyszed using the three criterion defined above. Keystone Clades were defined from the Keystone OTUs using clade definitions as outlined in Example 1. Keystone OTUs are reported in Table 9. Importantly, we identified the absence of Keystone OTUs in multiple particular disease states, indicating that bacterial compositions comprised of specific sets of Keystone OTUs are likely to have utility in multiple disease indications.

Demonstration that Keystone OTUs inhibit C. difficile Growth in a Competitive In Vitro Simulation Assay

To screen the ability of binary combinations comprising at least one Keystone OTU (binary pairs) to inhibit the growth of Clostridium difficile in vitro, vials of −80° C. glycerol stock banks of each OTU were thawed and diluted to 1e8 CFU/mL. Each strain was then diluted 10× (to a final concentration of 1e7 CFU/mL of each strain) into 200 uL of PBS+15% glycerol in the wells of a 96-well plate. Plates were then frozen at −80° C. When needed for the assay, plates were removed from −80° C. and thawed at room temperature under anaerobic conditions prior to use.

An overnight culture of Clostridium difficile was grown under anaerobic conditions in SweetB-FosIn or other suitable media for the growth of C. difficile. SweetB-FosIn is a complex media composed of brain heart infusion, yeast extract, cysteine, cellobiose, maltose, soluble starch, and fructooligosaccharides/inulin, and hemin, and is buffered with morpholino-propane sulphonic acid (MOPS). After 24 hr of growth the culture was diluted 100,000 fold into SweetB-FosIn. The diluted C. difficile mixture was then aliquoted to wells of a 96-well plate (180 uL to each well). 20 uL of a unique binary pair of Keystone OTUs was then added to each well at a final concentration of 1e6 CFU/mL of each species. Alternatively the assay can be tested with binary pairs at different initial concentrations (1e9 CFU/mL, 1e8 CFU/mL, 1e7 CFU/mL, 1e5 CFU/mL, 1e4 CFU/mL, 1e3 CFU/mL, 1e2 CFU/mL). Control wells only inoculated with C. difficile were included for a comparison to the growth of C. difficile without inhibition. Additional wells were used for controls that either inhibit or do not inhibit the growth of C. difficile. Plates were wrapped with parafilm and incubated for 24 hr at 37° C. under anaerobic conditions. After 24 hr the wells containing C. difficile alone were serially diluted and plated to determine titer on selective media such as CCFA (Anaerobe Systems) or CDSA (Becton Dickinson). The 96-well plate was then frozen at −80° C. before quantifying C. difficile by qPCR.

C. difficile in each well was quantified by qPCR. A standard curve was generated from a well on each assay plate containing only pathogenic C. difficile grown in SweetB+FosIn media as provided herein and compare to the microbiological titer determined above. Genomic DNA was extracted from the standard curve samples along with the other wells. Genomic DNA was extracted from 5 μl of each sample using a dilution, freeze/thaw, and heat lysis protocol. 5 μL of thawed samples were added to 45 μL of UltraPure water (Life Technologies, Carlsbad, Calif.) and mixed by pipetting. The plates with diluted samples were frozen at −20° C. until use for qPCR which includes a heated lysis step prior to amplification. Alternatively the genomic DNA could be isolated using the Mo Bio Powersoil®-htp 96 Well Soil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), Mo Bio Powersoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), or the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia, Calif.) according to the manufacturer's instructions.

The qPCR reaction mixture contained 1× SsoAdvanced Universal Probes Supermix, 900 nM of Wr-tcdB-F primer (AGCAGTTGAATATAGTGGTTTAGTTAGAGTTG (SEQ ID NO: 2044), IDT, Coralville, Iowa), 900 nM of Wr-tcdB-R primer (CATGCTTTTTTAGTTTCTGGATTGAA (SEQ ID NO: 2045), IDT, Coralville, Iowa), 250 nM of Wr-tcdB-P probe (6FAM-CATCCAGTCTCAATTGTATATGTTTCTCCA-MGB (SEQ ID NO. 2046), Life Technologies, Grand Island, N.Y.), and Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) to 18 μl (Primers adapted from: Wroblewski, D. et al., Rapid Molecular Characterization of Clostridium difficile and Assessment of Populations of C. difficile in Stool Specimens, Journal of Clinical Microbiology 47:2142-2148 (2009)). This reaction mixture was aliquoted to wells of a Hard-shell Low-Profile Thin Wall 96-well Skirted PCR Plate (BioRad, Hercules, Calif.). To this reaction mixture, 2 μl of diluted, frozen, and thawed samples were added and the plate sealed with a Microseal ‘B’ Adhesive Seal (BioRad, Hercules, Calif.). The qPCR was performed on a BioRad C1000™ Thermal Cycler equipped with a CFX96™ Real-Time System (BioRad, Hercules, Calif.). The thermocycling conditions were 95° C. for 15 minutes followed by 45 cycles of 95° C. for 5 seconds, 60° C. for 30 seconds, and fluorescent readings of the FAM channel. Alternatively, the qPCR could be performed with other standard methods known to those skilled in the art.

The Cq value for each well on the FAM channel was determined by the CFX Manager™ 3.0 software. The log 10(cfu/mL) of C. difficile each experimental sample was calculated by inputting a given sample's Cq value into a linear regression model generated from the standard curve comparing the Cq values of the standard curve wells to the known log 10(cfu/mL) of those samples. The log inhibition was calculated for each sample by subtracting the log 10(cfu/mL) of C. difficile in the sample from the log 10(cfu/mL) of C. difficile in the sample on each assay plate used for the generation of the standard curve that has no additional bacteria added. The mean log inhibition was calculated for all replicates for each composition.

A histogram of the range and standard deviation of each composition was plotted. Ranges or standard deviations of the log inhibitions that were distinct from the overall distribution were examined as possible outliers. If the removal of a single log inhibition datum from one of the binary pairs that were identified in the histograms would bring the range or standard deviation in line with those from the majority of the samples, that datum was removed as an outlier, and the mean log inhibition was recalculated.

The pooled variance of all samples evaluated in the assay was estimated as the average of the sample variances weighted by the sample's degrees of freedom. The pooled standard error was then calculated as the square root of the pooled variance divided by the square root of the number of samples. Confidence intervals for the null hypothesis were determined by multiplying the pooled standard error to the z score corresponding to a given percentage threshold. Mean log inhibitions outside the confidence interval were considered to be inhibitory if positive or stimulatory if negative with the percent confidence corresponding to the interval used. Samples with mean log inhibition greater than the 99% confidence interval (C.I) of the null hypothesis are reported as ++++, those with a 95%<C.I.<99% as +++, those with a 90%<C.I.<95% as ++, those with a 80%<C.I.<90% as + while samples with mean log inhibition less than than the 99% confidence interval (C.I) of the null hypothesis are reported as −−−−, those with a 95%<C.I.<99% as −−−, those with a 90%<C.I.<95% as −−, those with a 80%<C.I.<90% as −. Many binary pairs comprising Keystone OTUs inhibit C. difficile as delineated in Table 20.

Assignment of a Network Classes Based on Phylogenetic Diversity and Functional Modalities

“Network Classes” can be delineated by clustering computationally determined network ecologies into groupings based on the OTUs observed in a given network. In one example, OTUs are treated individualistically with each OTU representing a unique entity within the network. In other examples, the OTUs are clustered according to their phylogenetic relationships defined by a phylogenetic tree, e.g., into clades. In yet another embodiment, functional modules such as but not limited to KEGG Orthology Pathways can be used to cluster the networks, OTUs and Clades according to the biological or biochemical functions they comprise. A set of ecological networks from which a Network Class is defined, is selected using one or a combination of the following criteria: (i) networks that are derived from a biological phenotype, (ii) the frequency at which a given network is observed across samples, or (iii) the size of the network. In one embodiment, the required thresholds for the frequency at which a given network is observed across subject samples, and the size of a given network to be considered for further analysis are defined by the 50^(th), 70^(th), 80^(th), or 90^(th) percentiles of the distribution of these variables. In another embodiment, the required thresholds are defined by the value for a given variable that is significantly different from the mean or median value for a given variable using standard parametric or non-parametric measures of statistical significance. In yet another embodiment, ecological networks derived from Network Classes are selected that contain 5 or fewer, 10 or fewer, 15 or fewer, 20 or fewer, 25 or fewer, or 50 or fewer OTUs, Clades, or Functional modalities.

Network Class ecologies are defined using a heatmap analytical strategy whereby the OTU content of a given network is mapped relative to the networks in which it exists (See, e.g., FIG. 18). FIG. 18 is a Derivation of Network Ecology Classes, according to an embodiment of the invention. Subsets of networks are selected for use in defining Network Classes based on key biological criteria. Hierarchical Network clusters are defined by the presence (white) and absence (blue (or dark color)) of OTUs and/or Functional Metabolic Pathways and Classes are defined as branches of the hierarchical clustering tree based on the topological overlap measure.

Both OTUs comprising the network ecologies and the network ecologies themselves are ordered using a dendrogram that represents the relatedness of each OTU to every other OTU, or each Network Ecology to every other Network Ecology. The dendrogram for OTUs can be constructed using various clustering algorithms including but not limited to phylogenetic maximum likelihood, hierarchical clustering, or k-means clustering. In one embodiment, each row in the heatmap represents a single OTU, each column represents a Network Ecology and the color in the heatmap at a given row/column intersection represents whether the given OTU is present or absent in the given network. In another embodiment, the color in the heatmap represents the summed number of occurrences of the OTU in a set of related networks, represented as a cluster in the dendrogram of network ecologies. In another embodiment, the row and column intersections represent a summary variable calculated from the collapse of multiple rows and/or columns at selected nodes in the dendrograms. Network Classes are defined finding significant branch points in the hierarchical dendrogram. In one embodiment these branch points are defined as branches of the hierarchical clustering tree based on the topological overlap measure; this measure is a highly robust measure of network interconnectedness (Langfelder P, Zhang B, Horvath S. 2008. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24: 719-720.). Network Classes are defined based on OTU presence/absence or presence/absence and frequency patterns in network clusters; these patterns can be defined using specific OTUs, taxonomic groupings, or phylogenetic clades defined by the phylogenetically derived dendrogram (i.e. phylogenetic tree). Network Classes can be defined with the intent of maximizing the phylogenetic diversity of the class, and/or representing specific regions of functional relevance on the phylogenetic tree.

We defined a set of Network Classes for the Network Ecologies reported in Table 8 that were computationally inferred from health and disease datasets tied to CDAD studies using the method described above. We defined six Network Classes for these network ecologies (FIG. 18 and Tables 12-13).

Example 7. Biologically-Informed Optimization of Network Ecologies Based on Biological Properties

Network Ecologies can be optimized to have specific biological properties including but not limited to being of specific size (as example a specific number or OTUs); having a frequency of being observed in a population of healthy individuals (i.e. pervasiveness); having a certain percentage of spore forming OTUs as constituents; having a certain percentage of Keystone OTUs, clades or functions; having a defined phylogenetic breadth (as example defined by the total evolutionary distance spanned on a tree by the constituent members, or by the total number of genera or other taxonomic unit); or comprising specific functional capabilities such as but not limited to the ability metabolize secondary bile acids, or produce short chain fatty acids (SCFAs), or the biological intersection in which network ecology falls in a comparative phenotype map (see FIG. 19). The constituents of a network ecology can be optimized using both computational means as well as experimental means.

In one embodiment, we developed a biopriority score for networks that was computationally derived. This algorithm took the form of [F1*W1]+[F2*W2]+[F3*W3]+[F4*W4] where F is a biological criteria of interest and W is a weighting for that factor based on its importance to the derivation of the target network ecology. As example, if having a network with phylogenetic breadth was important one would weight this factor greater than the other factors. We developed a biopriority score that took into consideration the biological intersection of the network (FIG. 19), phylogenetic breadth, the pervasiveness or prevalence of the network in populations of healthy individuals, and the percentage of OTUs in the network that were Keystone OTUs. Network Ecologies reported in Table 8 were ranked based on this scoring and networks with a high score were preferentially screened and in vivo mouse model of C. difficile infection (Table 16).

In another embodiment we used a phylogenetic method paired with empirical testing to optimize the network ecologies for efficacy for the treatment of CDAD. Based on computational insights from our network analysis (Table 8), applicants defined Keystone Clades that represent specific phylogenetic clusters of OTUs. Applicants constructed various bacterial compositions using the methods described in Example 9 below, whereby applicants varied the phylogenetic breadth of the network ecologies based on the inclusion or exclusion of OTUs from specific clades. To test the effect of these variations on efficacy, 11 networks that feature clade substitutions, additions, or subtractions were tested at the same target dose of 1e7 CFU per OTU per animal in the mouse model of C. difficile infection experiment SP-376 (see Example 13 and Table 16). FIG. 3 provides an overview of the various clade substitutions or removals

The removal of clades 494 & 537 and the addition of clade_444 from network N1962, which was highly efficacious in protecting from symptoms of C. difficile infection with no mortality, yields network N1991, which was still largely protective of weight loss, but had increased mean maximum clinical scores relative to N1962.

N1990 adds clades 444 & 478 to N1962, and resulted in decreased mean minimum relative weight and increased mean maximum clinical scores relative to N1962 while remaining efficacious relative to the experiment's vehicle control.

Removal of clades 252 & 253 and the addition of clades 444 & 478 from N1962 produces N1975, which has increased mortality, decreased mean minimum relative weight and increased mean maximum clinical scores relative to N1962, which is only slightly less efficacious than the vehicle control.

The optimization of network ecologies to design microbiome therapeutics (as example a composition comprised of bacterial OTUs) with particular biological properties and features is executed using the strategy of having a core Backbone Network Ecology onto which R-Groups are added or subtracted to design toward particular characteristics. The Backbone forms a foundational composition of organisms or functions that are core to efficacy and need be present to observe efficacy. On this backbone one can make various compositional modifications using R-groups. R-Groups can be defined in multiple terms including but not limited to: individual OTUs, individual or multiple OTUs derived from a specific phylogenetic clade, and functional modalities comprised of multiple functional pathways and/or specific metabolic pathways. In other embodiments, R-groups could be considered prebiotics and other co-factors that are design into, or administered with a network ecology to promote specific biological properties.

Example 8. Network Analysis Across Multiple Data Sets and Selection of Target Network Ecologies with Capacity to Sporulate

One can select Network Ecologies and/or Network Class Ecologies as lead targets by defining networks with a specific biological function or activity such as sporulation. Networks Ecologies or Network Class Ecologies are first selected as described above and in Example 5 and 6. In one example, all Network Ecologies or Network Class Ecologies that contain at least one OTU that is capable of forming spores are targeted. In another example, all Network Ecologies or Network Class Ecologies that contain at least one OTU that is capable of forming spores, and that are comprised of at least 50%, 75%, or 100% Keystone OTUs are targeted. Keystone OTUs are selected as described above and in Example 6. OTUs are defined as spore formers using either phenotypic assays (see e.g. Stackebrandt and Hippe. Taxonomy and Systematics. In Clostridia. Biotechnology and Medical Applications.) or genetic assays (see e.g. Abecasis A B, Serrano M, Alves R, Quintais L, Pereira-Leal J B, and Henriques A O. 2013. A genomic signature and the identification of new sporulation genes. J. Bacteriol.; Paredes-Sabja D, Setlow P, and Sarker M R. 2011. Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved. Trends Microbiol. 19: 85-94). Exemplary network ecologies that are comprised of spore formers are illustrated in Tablell.

Example 9. Construction of Defined Ecobiotic Compositions

Source of Microbial Cultures. Pure cultures of organisms are isolated from the stool, oral cavity or other niche of the body of clinically qualified donors (as in Example 10) that contains microorganisms of interest using microbiological methods including those described below, and as are known to those skilled in the art. Alternatively, pure cultures are sourced from repositories such as the ATCC (atcc.org) or the DSMZ (dsmz.de/) which preserve and distribute cultures of bacteria, yeasts, phages, cell lines and other biological materials.

Enrichment and Purification of Bacteria. To purify individual bacterial strains, dilution plates were selected in which the density enables distinct separation of single colonies. Colonies were picked with a sterile implement (either a sterile loop or toothpick) and re-streaked to BBA or other solid media. Plates were incubated at 37° C. for 3-7 days. One or more well-isolated single colonies of the major morphology type were re-streaked. This process was repeated at least three times until a single, stable colony morphology is observed. The isolated microbe was then cultured anaerobically in liquid media for 24 hours or longer to obtain a pure culture of 106-1010 cfu/ml. Liquid growth medium might include Brain Heart Infusion-based medium (Atlas, Handbook of Microbiological Media, 4th ed, ASM Press, 2010) supplemented with yeast extract, hemin, cysteine, and carbohydrates (for example, maltose, cellobiose, soluble starch) or other media described previously. The culture was centrifuged at 10,000×g for 5 min to pellet the bacteria, the spent culture media was removed, and the bacteria were resuspended in sterile PBS. Sterile 75% glycerol was added to a final concentration of 20%. An aliquot of glycerol stock was titered by serial dilution and plating. The remainder of the stock was frozen on dry ice for 10-15 min and then placed at −80° C. for long term storage.

Cell Bank Preparation

Cell banks (RCBs) of bacterial strains were prepared as follows. Bacterial strains were struck from −80° C. frozen glycerol stocks to Brucella blood agar with Hemin or Vitamin K (Atlas, Handbook of Microbiological Media, 4th ed, ASM Press, 2010), M2GSC (Atlas, Handbook of Microbiological Media, 4th ed, ASM Press, 2010) or other solid growth media and incubated for 24 to 48 h at 37° C. in an anaerobic chamber with a gas mixture of H2:CO2:N2 of 10:10:80. Single colonies were then picked and used to inoculate 250 ml to 1 L of Wilkins-Chalgren broth, Brain-Heart Infusion broth, M2GSC broth or other growth media, and grown to mid to late exponential phase or into the stationary phase of growth. Alternatively, the single colonies may be used to inoculate a pilot culture of 10 ml, which were then used to inoculate a large volume culture. The growth media and the growth phase at harvest were selected to enhance cell titer, sporulation (if desired) and phenotypes that might be associated desired in vitro or in vivo. Optionally, cultures were grown static or shaking, depending which yielded maximal cell titer. The cultures were then concentrated 10 fold or more by centrifugation at 5000 rpm for 20 min, and resuspended in sterile phosphate buffered saline (PBS) plus 15% glycerol. 1 ml aliquots were transferred into 1.8 ml cryovials which were then frozen on dry ice and stored at −80° C. The identity of a given cell bank was confirmed by PCR amplification of the 16S rDNA gene, followed by Sanger direct cycle sequencing. See Examples 1, 2. Each bank was confirmed to yield colonies of a single morphology upon streaking to Brucella blood agar or M2GSC agar. When more than one morphology was observed, colonies were confirmed to be the expected species by PCR and sequencing analysis of the 16S rDNA gene. Variant colony morphologies can be observed within pure cultures, and in a variety of bacteria the mechanisms of varying colony morphologies have been well described (van der Woude, Clinical Microbiology Reviews, 17:518, 2004), including in Clostridium species (Wadsworth-KTL Anaerobic Bacteriology Manual, 6th Ed, Jousimie-Somer, et al 2002). For obligate anaerobes, RCBs were confirmed to lack aerobic colony forming units at a limit of detection of 10 cfu/ml.

Titer Determination

The number of viable cells per ml was determined on the freshly harvested, washed and concentrated culture by plating serial dilutions of the RCB to Brucella blood agar or other solid media, and varied from 106 to 1010 cfu/ml. The impact of freezing on viability was determined by titering the banks after one or two freeze-thaw cycles on dry ice or at −80° C., followed by thawing in an anaerobic chamber at room temperature. Some strains displayed a 1-3 log drop in viable cfu/ml after the 1st and/or 2nd freeze thaw, while the viability of others were unaffected.

Preparation of Bacterial Compositions

Individual strains were typically thawed on ice and combined in an anaerobic chamber to create mixtures, followed by a second freeze at −80° C. to preserve the mixed samples. When making combinations of strains for in vitro or in vivo assays, the cfu in the final mixture was estimated based on the second freeze-thaw titer of the individual strains. For experiments in rodents, strains may be combined at equal counts in order to deliver between 1e4 and 1e10 per strain. Additionally, some bacteria may not grow to sufficient titer to yield cell banks that allowed the production of compositions where all bacteria were present at 1e10.

Selection of Media for Growth

Provided are appropriate media to support growth, including preferred carbon sources. For example, some organisms prefer complex sugars such as cellobiose over simple sugars. Examples of media used in the isolation of sporulating organisms include EYA, BHI, BHIS, and GAM (see below for complete names and references). Multiple dilutions are plated out to ensure that some plates will have well isolated colonies on them for analysis, or alternatively plates with dense colonies may scraped and suspended in PBS to generate a mixed diverse community.

Plates are incubated anaerobically or aerobically at 37° C. for 48-72 or more hours, targeting anaerobic or aerobic spore formers, respectively.

Solid plate media include:

-   -   Gifu Anaerobic Medium (GAM, Nissui) without dextrose         supplemented with fructooligosaccharides/inulin (0.4%), mannitol         (0.4%), inulin (0.4%), or fructose (0.4%), or a combination         thereof     -   Sweet GAM [Gifu Anaerobic Medium (GAM, Nissui)] modified,         supplemented with glucose, cellobiose, maltose, L-arabinose,         fructose, fructooligosaccharides/inulin, mannitol and sodium         lactate)     -   Brucella Blood Agar (BBA, Atlas, Handbook of Microbiological         Media, 4th ed, ASM Press, 2010)     -   PEA sheep blood (Anaerobe Systems; 5% Sheep Blood Agar with         Phenylethyl Alcohol)     -   Egg Yolk Agar (EYA) (Atlas, Handbook of Microbiological Media,         4th ed, ASM Press, 2010)     -   Sulfite polymyxin milk agar (Mevissen-Verhage et al., J. Clin.         Microbiol. 25:285-289 (1987))     -   Mucin agar (Derrien et al., IJSEM 54: 1469-1476 (2004))     -   Polygalacturonate agar (Jensen & Canale-Parola, Appl. Environ.         Microbiol. 52:880-997 (1986))     -   M2GSC (Atlas, Handbook of Microbiological Media, 4th ed, ASM         Press, 2010)     -   M2 agar (Atlas, Handbook of Microbiological Media, 4th ed, ASM         Press, 2010) supplemented with starch (1%), mannitol (0.4%),         lactate (1.5 g/L) or lactose (0.4%)     -   Sweet B—Brain Heart Infusion agar (Atlas, Handbook of         Microbiological Media, 4th ed, ASM Press, 2010) supplemented         with yeast extract (0.5%), hemin, cysteine (0.1%), maltose         (0.1%), cellobiose (0.1%), soluble starch (sigma, 1%), MOPS (50         mM, pH 7).     -   PY-salicin (peptone-yeast extract agar supplemented with         salicin) (Atlas, Handbook of Microbiological Media, 4th ed, ASM         Press, 2010).     -   Modified Brain Heart Infusion (M-BHI) [[sweet and sour]]         contains the following per L: 37.5 g Brain Heart Infusion powder         (Remel), 5 g yeast extract, 2.2 g meat extract, 1.2 g liver         extract, 1 g cystein HCl, 0.3 g sodium thioglycolate, 10 mg         hemin, 2 g soluble starch, 2 g FOS/Inulin, 1 g cellobiose, 1 g         L-arabinose, 1 g mannitol, 1 Na-lactate, 1 mL Tween 80, 0.6 g         MgSO4×7H2O, 0.6 g CaCl2, 6 g (NH4)2SO4, 3 g KH2PO4, 0.5 g         K2HPO4, 33 mM Acetic acid, 9 mM propionic acid, 1 mM Isobutyric         acid, 1 mM isovaleric acid, 15 g agar, and after autoclaving add         50 mL of 8% NaHCO₃ solution and 50 mL 1M MOPS-KOH (pH 7).     -   Noack-Blaut Eubacterium agar (See Noack et al. J. Nutr. (1998)         128:1385-1391)     -   BHIS az1/ge2—BHIS az/ge agar (Reeves et. al. Infect. Immun.         80:3786-3794 (2012)) [Brain Heart Infusion agar (Atlas, Handbook         of Microbiological Media, 4th ed, ASM Press, 2010) supplemented         with yeast extract 0.5%, cysteine 0.1%, 0.1% cellobiose, 0.1%         inulin, 0.1% maltose, aztreonam 1 mg/L, gentamycin 2 mg/L]     -   BHIS CInM az1/ge2—BHIS CInM [Brain Heart Infusion agar (Atlas,         Handbook of Microbiological Media, 4th ed, ASM Press, 2010)         supplemented with yeast extract 0.5%, cysteine 0.1%, 0.1%         cellobiose, 0.1% inulin, 0.1% maltose, aztreonam 1 mg/L,         gentamycin 2 mg/L].

Method of Preparing the Bacterial Composition for Administration to a Patient

Two strains for the bacterial composition are independently cultured and mixed together before administration. Both strains are independently be grown at 37° C., pH 7, in a GMM or other animal-products-free medium, pre-reduced with 1 g/L cysteine ŸHCl. After each strain reaches a sufficient biomass, it is preserved for banking by adding 15% glycerol and then frozen at −80° C. in 1 ml cryotubes.

Each strain is then be cultivated to a concentration of 1010 CFU/mL, then concentrated 20-fold by tangential flow microfiltration; the spent medium is exchanged by diafiltering with a preservative medium consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium phosphate buffer, or other suitable preservative medium. The suspension is freeze-dried to a powder and titrated.

After drying, the powder is blended with microcrystalline cellulose and magnesium stearate and formulated into a 250 mg gelatin capsule containing 10 mg of lyophilized powder (108 to 1011 bacteria), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate.

Example 10. Construction and Administration of an Ethanol-Treated Spore Preparation

Provision of fecal material. Fresh fecal samples were obtained from healthy human donors who have been screened for general good health and for the absence of infectious diseases, and meet inclusion and exclusion criteria, inclusion criteria include being in good general health, without significant medical history, physical examination findings, or clinical laboratory abnormalities, regular bowel movements with stool appearance typically Type 2, 3, 4, 5 or 6 on the Bristol Stool Scale, and having a BMI≥18 kg/m2 and ≤25 kg/m2. Exclusion criteria generally included significant chronic or acute medical conditions including renal, hepatic, pulmonary, gastrointestinal, cardiovascular, genitourinary, endocrine, immunologic, metabolic, neurologic or hematological disease, a family history of, inflammatory bowel disease including Crohn's disease and ulcerative colitis, Irritable bowel syndrome, colon, stomach or other gastrointestinal malignancies, or gastrointestinal polyposis syndromes, or recent use of yogurt or commercial probiotic materials in which an organism(s) is a primary component. Non-related donors were screened for general health history for absence of chronic medical conditions (including inflammatory bowel disease; irritable bowel syndrome; Celiac disease; or any history of gastrointestinal malignancy or polyposis), absence of risk factors for transmissible infections, antibiotic non-use in the previous 6 months, and negative results in laboratory assays for blood-borne pathogens (HIV, HTLV, HCV, HBV, CMV, HAV and Treponema pallidum) and fecal bacterial pathogens (Salmonella, Shigella, Yersinia, Campylobacter, E. coli 0157), ova and parasites, and other infectious agents (Giardia, Cryptosporidium, Cyclospora, Isospora) prior to stool donation. Samples were collected directly using a commode specimen collection system, which contains a plastic support placed on the toilet seat and a collection container that rests on the support. Feces were deposited into the container, and the lid was then placed on the container and sealed tightly. The sample was then delivered on ice within 1-4 hours for processing. Samples were mixed with a sterile disposable tool, and 2-4 g aliquots were weighed and placed into tubes and flash frozen in a dry ice/ethanol bath. Aliquots are frozen at −80 degrees Celsius until use.

Optionally, the fecal material was suspended in a solution, and/or fibrous and/or particulate materials were removed using either filtration or centrifugation. A frozen aliquot containing a known weight of feces was removed from storage at −80° C. and allowed to thaw at room temperature. Sterile 1×PBS was added to create a 10% w/v suspension, and vigorous vortexing was performed to suspend the fecal material until the material appeared homogeneous. The material was then left to sit for 10 minutes at room temperature to sediment fibrous and particulate matter. The suspension above the sediment was then carefully removed into a new tube and contains a purified spore population. Optionally, the suspension was then centrifuged at a low speed, e.g., 1000×g, for 5 minutes to pellet particulate matter including fibers. The pellet was discarded and the supernatant, which contained vegetative organisms and spores, was removed into a new tube. The supernatant was then centrifuged at 6000×g for 10 minutes to pellet the vegetative organisms and spores. The pellet was then resuspended in 1×PBS with vigorous vortexing until the material appears homogenous.

Generation of a Spore Preparation from Alcohol Treatment of Fecal Material

A 10% w/v suspension of human fecal material in PBS was filtered, centrifuged at low speed, and the supernate containing spores was mixed with absolute ethanol in a 1:1 ratio and vortexed to mix. The suspension was incubated at room temperature for 1 hour. After incubation the suspension was centrifuged at high speed to concentrate spores into a pellet containing a purified spore-containing preparation. The supernate was discarded and the pellet resuspended in an equal mass of glycerol, and the purified spore preparation was placed into capsules and stored at −80 degrees Celsius.

Characterization of Spores Content in Purified Spore Populations

In one embodiment, counts of viable spores are determined by performing 10 fold serial dilutions in PBS and plating to Brucella Blood Agar Petri plates or applicable solid media. Plates are incubated at 37 degrees Celsius for 2 days. Colonies are counted from a dilution plate with 50-400 colonies and used to back-calculate the number of viable spores in the population. The ability to germinate into vegetative bacteria is also demonstrated. Visual counts are determined by phase contrast microscopy. A spore preparation is either diluted in PBS or concentrated by centrifugation, and a 5 microliter aliquot is placed into a Petroff Hauser counting chamber for visualization at 400× magnification. Spores are counted within ten 0.05 mm×0.05 mm grids and an average spore count per grid is determined and used to calculate a spore count per ml of preparation. Lipopolysaccharide (LPS) reduction in purified spore populations is measured using a Limulus amebocyte lysate (LAL) assay such as the commercially available ToxinSensor™ Chromogenic LAL Endotoxin Assay Kit (GenScript, Piscataway, N.J.) or other standard methods known to those skilled in the art.

In a second embodiment, counts of spores are determined using a spore germination assay. Germinating a spore fraction increases the number of viable spores that will grow on various media types. To germinate a population of spores, the sample is moved to the anaerobic chamber, resuspended in prereduced PBS, mixed and incubated for 1 hour at 37° C. to allow for germination. Germinants can include amino-acids (e.g., alanine, glycine), sugars (e.g., fructose), nucleosides (e.g., inosine), bile salts (e.g., cholate and taurocholate), metal cations (e.g., Mg2+, Ca2+), fatty acids, and long-chain alkyl amines (e.g., dodecylamine, Germination of bacterial spores with alkyl primary amines” J. Bacteriology, 1961.). Mixtures of these or more complex natural mixtures, such as rumen fluid or Oxgall, can be used to induce germination. Oxgall is dehydrated bovine bile composed of fatty acids, bile acids, inorganic salts, sulfates, bile pigments, cholesterol, mucin, lecithin, glycuronic acids, porphyrins, and urea. The germination can also be performed in a growth medium like prereduced BHIS/oxgall germination medium, in which BHIS (Brain heart infusion powder (37 g/L), yeast extract (5 g/L), L-cysteine HCl (1 g/L)) provides peptides, amino acids, inorganic ions and sugars in the complex BHI and yeast extract mixtures and Oxgall provides additional bile acid germinants.

In addition, pressure may be used to germinate spores. The selection of germinants can vary with the microbe being sought. Different species require different germinants and different isolates of the same species can require different germinants for optimal germination. Finally, it is important to dilute the mixture prior to plating because some germinants are inhibitory to growth of the vegetative-state microorganisms. For instance, it has been shown that alkyl amines must be neutralized with anionic lipophiles in order to promote optimal growth. Bile acids can also inhibit growth of some organisms despite promoting their germination, and must be diluted away prior to plating for viable cells.

For example, BHIS/oxgall solution is used as a germinant and contains 0.5×BHIS medium with 0.25% oxgall (dehydrated bovine bile) where 1×BHIS medium contains the following per L of solution: 6 g Brain Heart Infusion from solids, 7 g peptic digest of animal tissue, 14.5 g of pancreatic digest of casein, 5 g of yeast extract, 5 g sodium chloride, 2 g glucose, 2.5 g disodium phosphate, and 1 g cysteine. Additionally, Ca-DPA is a germinant and contains 40 mM CaCl2, and 40 mM dipicolinic acid (DPA). Rumen fluid (Bar Diamond, Inc.) is also a germinant. Simulated gastric fluid (Ricca Chemical) is a germinant and is 0.2% (w/v) Sodium Chloride in 0.7% (v/v) Hydrochloric Acid. Mucin medium is a germinant and prepared by adding the following items to 1 L of distilled sterile water: 0.4 g KH2PO4, 0.53 g Na2HPO4, 0.3 g NH4Cl, 0.3 g NaCl, 0.1 g MgCl2×6H2O, 0.11 g CaCl2, 1 ml alkaline trace element solution, 1 ml acid trace element solution, 1 ml vitamin solution, 0.5 mg resazurin, 4 g NaHCO3, 0.25 g Na2S×9 H2O. The trace element and vitamin solutions prepared as described previously (Stams et al., 1993). All compounds were autoclaved, except the vitamins, which were filter-sterilized. The basal medium was supplemented with 0.7% (v/v) clarified, sterile rumen fluid and 0.25% (v/v) commercial hog gastric mucin (Type III; Sigma), purified by ethanol precipitation as described previously (Miller & Hoskins, 1981). This medium is referred herein as mucin medium.

Fetal Bovine Serum (Gibco) can be used as a germinant and contains 5% FBS heat inactivated, in Phosphate Buffered Saline (PBS, Fisher Scientific) containing 0.137M Sodium Chloride, 0.0027M Potassium Chloride, 0.0119M Phosphate Buffer. Thioglycollate is a germinant as described previously (Kamiya et al Journal of Medical Microbiology 1989) and contains 0.25M (pH10) sodium thioglycollate. Dodecylamine solution containing 1 mM dodecylamine in PBS is a germinant. A sugar solution can be used as a germinant and contains 0.2% fructose, 0.2% glucose, and 0.2% mannitol. Amino acid solution can also be used as a germinant and contains 5 mM alanine, 1 mM arginine, 1 mM histidine, 1 mM lysine, 1 mM proline, 1 mM asparagine, 1 mM aspartic acid, 1 mM phenylalanine. A germinant mixture referred to herein as Germix 3 can be a germinant and contains 5 mM alanine, 1 mM arginine, 1 mM histidine, 1 mM lysine, 1 mM proline, 1 mM asparagine, 1 mM aspartic acid, 1 mM phenylalanine, 0.2% taurocholate, 0.2% fructose, 0.2% mannitol, 0.2% glucose, 1 mM inosine, 2.5 mM Ca-DPA, and 5 mM KCl. BHIS medium+DPA is a germinant mixture and contains BHIS medium and 2 mM Ca-DPA. Escherichia coli spent medium supernatant referred to herein as EcSN is a germinant and is prepared by growing E. coli MG1655 in SweetB/Fos inulin medium anaerobically for 48 hr, spinning down cells at 20,000 rcf for 20 minutes, collecting the supernatant and heating to 60 C for 40 min. Finally, the solution is filter sterilized and used as a germinant solution.

Determination of Bacterial Pathogens In Purified Spore Populations

Bacterial pathogens present in a purified spore population are determined by qPCR using specific oligonucleotide primers as follows.

Standard Curve Preparation

The standard curve is generated from wells containing the pathogen of interest at a known concentration or simultaneously quantified by selective spot plating. Serial dilutions of duplicate cultures are performed in sterile phosphate-buffered saline. Genomic DNA is then extracted from the standard curve samples along with the other samples.

Genomic DNA Extraction

Genomic DNA may be extracted from 100 μl of fecal samples, fecal-derived samples, or purified spore preparations using the Mo Bio Powersoil®-htp 96 Well Soil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.) according to the manufacturer's instructions with two exceptions: the beadbeating is performed for 2×4:40 minutes using a BioSpec Mini-Beadbeater-96 (BioSpec Products, Bartlesville, OK) and the DNA is eluted in 50 μl of Solution C6. Alternatively the genomic DNA could be isolated using the Mo Bio Powersoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), the Sigma-Aldrich Extract-N-Amp™Plant PCR Kit, the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia, Calif.) according to the manufacturer's instructions.

qPCR Composition and Conditions

The qPCR reaction to detect C. difficile contains 1× HotMasterMix (5PRIME, Gaithersburg, Md.), 900 nM of Wr-tcdB-F (AGCAGTTGAATATAGTGGTTTAGTTAGAGTTG (SEQ ID NO. 2044), IDT, Coralville, Iowa), 900 nM of Wr-tcdB-R (CATGCTTTTTTAGTTTCTGGATTGAA (SEQ ID NO. 2045), IDT, Coralville, Iowa), 250 nM of We-tcdB-P (6FAM-CATCCAGTCTCAATTGTATATGTTTCTCCA-MGB (SEQ ID NO. 2046), Life Technologies, Grand Island, N.Y.), and PCR Water (Mo Bio Laboratories, Carlsbad, Calif.) to 18 μl (Primers adaped from: Wroblewski, D. et al. Rapid Molecular Characterization of Clostridium difficile and Assessment of Populations of C. difficile in Stool Specimens. Journal of Clinical Microbiology 47:2142-2148 (2009)). This reaction mixture is aliquoted to wells of a MicroAmp® Fast Optical 96-well Reaction Plate with Barcode (0.1 mL) (Life Technologies, Grand Island, N.Y.). To this reaction mixture, 2 μl of extracted genomic DNA is added. The qPCR is performed on a BioRad C1000™ Thermal Cycler equipped with a CFX96™ Real-Time System (BioRad, Hercules, Calif.). The thermocycling conditions are 95° C. for 2 minutes followed by 45 cycles of 95° C. for 3 seconds, 60° C. for 30 seconds, and fluorescent readings of the FAM and ROX channels. Other bacterial pathogens can be detected by using primers and a probe specific for the pathogen of interest.

Data Analysis

The Cq value for each well on the FAM channel is determined by the CFX Manager™ Software Version 2.1. The log 10(cfu/ml) of each experimental sample is calculated by inputting a given sample's Cq value into linear regression model generated from the standard curve comparing the Cq values of the standard curve wells to the known log 10(cfu/ml) of those samples. Viral pathogens present in a purified spore population are determined by qPCR as described herein and otherwise known in the art.

Example 11. Characterization of Microbiome in Ethanol-Treated Spore Population and Patients Post-Treatment Microbial Population Engraftment, Augmentation, and Reduction of Pathogen Carriage in Patients Treated with Spore Compositions

Complementary genomic and microbiological methods were used to characterize the composition of the microbiota from Patient 1, 2, 3, 4, and 5, 6, 7, 8, 9, and 10 at pretreatment (pretreatment) and up to 4 weeks post-treatment.

Table 3 shows bacterial OTUs associated with engraftment and ecological augmentation and establishment of a more diverse microbial ecology in patients treated with an ethanol-treated spore preparation. OTUs that comprise an augmented ecology are below the limit of detection in the patient prior to treatment and/or exist at extremely low frequencies such that they do not comprise a significant fraction of the total microbial carriage and are not detectable by genomic and/or microbiological assay methods in the bacterial composition. OTUs that are members of the engrafting and augmented ecologies were identified by characterizing the OTUs that increase in their relative abundance post treatment and that respectively are: (i) present in the ethanol-treated spore preparation and not detectable in the patient pretreatment (engrafting OTUs), or (ii) absent in the ethanol-treated spore preparation, but increase in their relative abundance in the patient through time post treatment with the preparation due to the formation of favorable growth conditions by the treatment (augmenting OTUs). Notably, the latter OTUs can grow from low frequency reservoirs in the patient, or be introduced from exogenous sources such as diet. OTUs that comprise a “core” augmented or engrafted ecology can be defined by the percentage of total patients in which they are observed to engraft and/or augment; the greater this percentage the more likely they are to be part of a core ecology responsible for catalyzing a shift away from a dysbiotic ecology. The dominant OTUs in an ecology can be identified using several methods including but not limited to defining the OTUs that have the greatest relative abundance in either the augmented or engrafted ecologies and defining a total relative abundance threshold. As example, the dominant OTUs in the augmented ecology of Patient-1 were identified by defining the OTUs with the greatest relative abundance, which together comprise 60% of the microbial carriage in this patient's augmented ecology by day 25 post-treatment.

Patient treatment with the ethanol-treated spore preparation leads to the population of a microbial ecology that has greater diversity than prior to treatment (See FIGS. 5 & 6). Genomic-based microbiome characterization confirmed engraftment of a range of OTUs that were not detectable in the patient pretreatment (Table 3). These OTUs comprised both bacterial species that were capable and not capable of forming spores, and OTUs that represent multiple phylogenetic clades. Organisms not detectable in Patient 1 pre-treatment either engraft directly from the ethanol-treated spore fraction or are augmented by the creation of a gut environment favoring a healthy, diverse microbiota. Microbiological analysis shows that Bacteroides fragilis group species were increased by 4 and 6 logs in patients 1 and 2 (FIG. 7).

FIG. 5 shows the microbial diversity measured in the ethanol-treated spore treatment sample and patient pre- and post-treatment samples. Total microbial diversity is defined using the Chaol Alpha-Diversity Index and is measured at different genomic sampling depths to confirm adequate sequence coverage to assay the microbiome in the target samples. The patient pretreatment (purple) harbored a microbiome that was significantly reduced in total diversity as compared to the ethanol-treated spore product (red) and patient post treatment at days 5 (blue), 14 (orange), and 25 (green).

FIG. 6 shows patient microbial ecology is shifted by treatment with an ethanol-treated spore treatment from a dysbiotic state to a state of health. Principal Coordinates Analysis based on the total diversity and structure of the microbiome (Bray-Curtis Beta-Diversity) of the patient pre- and post-treatment delineates that the engraftment of OTUs from the spore treatment and the augmentation of the patient microbial ecology leads to a microbial ecology that is distinct from both the pretreatment microbiome and the ecology of the ethanol-treated spore treatment (Table 3).

FIG. 7 shows the augmentation of Bacteroides species in patients. Comparing the number of Bacteroides fragilis groups species in feces (cfu/g) pre-treatment and in week 4 post treatment reveals an increase of 4 logs or greater. The ability of 16S-V4 OTU identification to assign an OTU as a specific species depends in part on the resolution of the 16S-V4 region of the 16S gene for a particular species or group of species. Both the density of available reference 16S sequences for different regions of the tree as well as the inherent variability in the 16S gene between different species will determine the definitiveness of a taxonomic annotation to a given sequence read. Given the topological nature of a phylogenetic tree and that the tree represents hierarchical relationships of OTUs to one another based on their sequence similarity and an underlying evolutionary model, taxonomic annotations of a read can be rolled up to a higher level using a clade-based assignment procedure (Table 1). Using this approach, clades are defined based on the topology of a phylogenetic tree that is constructed from full-length 16S sequences using maximum likelihood or other phylogenetic models familiar to individuals with ordinary skill in the art of phylogenetics. Clades are constructed to ensure that all OTUs in a given clade are: (i) within a specified number of bootstrap supported nodes from one another (generally, 1-5 bootstraps), and (ii) within a 5% genetic similarity. OTUs that are within the same clade can be distinguished as genetically and phylogenetically distinct from OTUs in a different clade based on 16S-V4 sequence data. OTUs falling within the same clade are evolutionarily closely related and may or may not be distinguishable from one another using 16S-V4 sequence data. The power of clade based analysis is that members of the same clade, due to their evolutionary relatedness, play similar functional roles in a microbial ecology such as that found in the human gut. Compositions substituting one species with another from the same clade are likely to have conserved ecological function and therefore are useful in the present invention.

Stool samples were aliquoted and resuspended 10× vol/wt in either 100% ethanol (for genomic characterization) or PBS containing 15% glycerol (for isolation of microbes) and then stored at −80° C. until needed for use. For genomic 16S sequence analysis colonies picked from plate isolates had their full-length 16S sequence characterized as described in Examples 2 and 3, and primary stool samples were prepared targeting the 16S-V4 region using the method for heterogeneous samples described herein.

Notably, 16S sequences of isolates of a given OTU are phylogenetically placed within their respective clades despite that the actual taxonomic assignment of species and genus may suggest they are taxonomically distinct from other members of the clades in which they fall. Discrepancies between taxonomic names given to an OTU is based on microbiological characteristics versus genetic sequencing are known to exist from the literature. The OTUs footnoted in this table are known to be discrepant between the different methods for assigning a taxonomic name.

Engraftment of OTUs from the ethanol-treated spore preparation treatment into the patient as well as the resulting augmentation of the resident microbiome led to a significant decrease in and elimination of the carriage of pathogenic species other than C. difficile in the patient. 16S-V4 sequencing of primary stool samples demonstrated that at pretreatment, 20% of reads were from the genus Klebsiella and an additional 19% were assigned to the genus Fusobacterium. These striking data are evidence of a profoundly dysbiotic microbiota associated with recurrent C. difficile infection and chronic antibiotic use. In healthy individuals, Klebsiella is a resident of the human microbiome in only about 2% of subjects based on an analysis of HMP database (hmpdacc.org), and the mean relative abundance of Klebsiella is only about 0.09% in the stool of these people. Its surprising presence at 20% relative abundance in Patient 1 before treatment is an indicator of a proinflammatory gut environment enabling a “pathobiont” to overgrow and outcompete the commensal organisms normally found in the gut. Similarly, the dramatic overgrowth of Fusobacterium indicates a profoundly dysbiotic gut microbiota. One species of Fusobacterium, F. nucleatum (an OTU phylogenetically indistinguishable from Fusobacterium sp. 3_1_33 based on 16S-V4), has been termed “an emerging gut pathogen” based on its association with IBD, Crohn's disease, and colorectal cancer in humans and its demonstrated causative role in the development of colorectal cancer in animal models [Allen-Vercoe, Gut Microbes (2011) 2:294-8]. Importantly, neither Klebsiella nor Fusobacterium was detected in the 16S-V4 reads by Day 25 (Table 4).

To further characterize the colonization of the gut by Klebsiella and other Enterobacteriaceae and to speciate these organisms, pretreatment and Day 25 fecal samples stored at −80 C as PBS-glycerol suspensions were plated on a variety of selective media including MacConkey lactose media (selective for gram negative enterobacteria) and Simmons Citrate Inositol media (selective for Klebsiella spp) [Van Cregten et al, J. Clin. Microbiol. (1984) 20: 936-41]. Enterobacteria identified in the patient samples included K. pneumoniae, Klebsiella sp. Co_9935 and E. coli. Strikingly, each Klebsiella species was reduced by 2-4 logs whereas E. coli, a normal commensal organism present in a healthy microbiota, was reduced by less than 1 log (Table 14 below). This decrease in Klebsiella spp. carriage is consistent across multiple patients. Four separate patients were evaluated for the presence of Klebsiella spp. pre treatment and 4 weeks post treatment. Klebsiella spp. were detected by growth on selective Simmons Citrate Inositol media as previously described. Serial dilution and plating, followed by determining cfu/mL titers of morphologically distinct species and 16S full length sequence identification of representatives of those distinct morphological classes, allowed calculation of titers of specific species.

The genus Bacteroides is an important member of the gastrointestinal microbiota; 100% of stool samples from the Human Microbiome Project contain at least one species of Bacteroides with total relative abundance in these samples ranging from 0.96% to 93.92% with a median relative abundance of 52.67% (hmpdacc.org reference data set HMSMCP). Bacteroides in the gut has been associated with amino acid fermentation and degradation of complex polysaccharides. Its presence in the gut is enhanced by diets rich in animal-derived products as found in the typical western diet [David, L. A. et al, Nature (2013) doi:10.1038/nature12820]. Strikingly, prior to treatment, fewer than 0.008% of the 16S-V4 reads from Patient 1 mapped to the genus Bacteroides strongly suggesting that Bacteroides species were absent or that viable Bacteroides were reduced to an extremely minor component of the patient's gut microbiome. Post treatment, ≥42% of the 16S-V4 reads could be assigned to the genus Bacteroides within 5 days of treatment and by Day 25 post treatment 59.48% of the patients gut microbiome was comprised of Bacteroides. These results were confirmed microbiologically by the absence of detectable Bacteroides in the pretreatment sample plated on two different Bacteroides selective media: Bacteroides Bile Esculin (BBE) agar which is selective for Bacteroides fragilis group species [Livingston, S. J. et al J. Clin. Microbiol (1978). 7: 448-453] and Polyamine Free Arabinose (PFA) agar [Noack et al. J. Nutr. (1998) 128: 1385-1391; modified by replacing glucose with arabinose]. The highly selective BBE agar had a limit of detection of <2×103 cfu/g, while the limit of detection for Bacteroides on PFA agar was approximately 2×107 cfu/g due to the growth of multiple non-Bacteroides species in the pretreatment sample on that medium. Colony counts of Bacteroides species on Day 25 were up to 2×1010 cfu/g, consistent with the 16S-V4 sequencing, demonstrating a profound reconstitution of the gut microbiota in Patient 1 (Table 5 below).

The significant abundance of Bacteroides in Patient 1 on Day 25 (and as early as Day 5 as shown by 16S-V4 sequencing) is remarkable. Viable Bacteroides fragilis group species were not present in the ethanol-treated spore population based on microbiological plating (limit of detection of 10 cfu/ml). Thus, administration of the ethanol-treated spore population to Patient 1 resulted in microbial population of the patient's GI tract, not only due to the engraftment of bacterial species such as but not limited to spore forming species, but also the restoration of high levels of non-spore forming species commonly found in healthy individuals through the creation of a niche that allowed for the repopulation of Bacteroides species. These organisms were most likely either present at extremely low abundance in the GI tract of Patient 1, or present in a reservoir in the GI tract from which they could rebound to high titer. Those species may also be reinoculated via oral uptake from food following treatment. We term this healthy repopulation of the gut with OTUs that are not present in the bacterial composition such as but not limited to a spore population or ethanol-treated spore population, “Augmentation.” Augmentation is an important phenomenon in that it shows the ability to use an ethanol-treated spore ecology or other bacterial composition to restore a healthy microbiota by seeding a diverse array or commensal organisms beyond the actual component organisms in the bacterial composition such as but not limited to an ethanol-treated spore population itself; specifically the spore composition treatment itself and the engraftment of OTUs from the spore composition create a niche that enables the outgrowth of OTUs required to shift a dysbiotic microbiome to a microbial ecology that is associated with health. The diversity of Bacteroides species and their approximate relative abundance in the gut of Patient 1 is shown in Table 16, comprising at least 8 different species.

FIG. 8 shows species engrafting versus species augmenting in patients microbiomes after treatment with a bacterial composition such as but not limited to an ethanol-treated spore population. Relative abundance of species that engrafted or augmented as described were determined based on the number of 16S sequence reads. Each plot is from a different patient treated with the bacterial composition such as but not limited to an ethanol-treated spore population for recurrent C. difficile.

The impact of the bacterial composition such as but not limited to an ethanol-treated spore population treatment on carriage of imipenem resistant Enterobacteriaceae was assessed by plating pretreatment and Day 28 clinical samples from Patients 2, 4 and 5 on MacConkey lactose plus 1 ug/mL of imipenem. Resistant organisms were scored by morphology, enumerated and DNA was submitted for full length 16S rDNA sequencing as described above. Isolates were identified as Morganella morganii, Providencia rettgeri and Proteus penneri. Each of these are gut commensal organisms; overgrowth can lead to bacteremia and/or urinary tract infections requiring aggressive antibiotic treatment and, in some cases, hospitalization [Kim, B-N, et al Scan J. Inf Dis (2003) 35: 98-103; Lee, I—K and Liu, J-W J. Microbiol Immunol Infect (2006) 39: 328-334; O'Hara et al, Clin Microbiol Rev (2000) 13: 534]. The titer of organisms at pretreatment and Day 28 by patient is shown in Table 17. Importantly, administration of the bacterial composition such as but not limited to an ethanol-treated spore preparation resulted in greater than 100-fold reduction in 4 of 5 cases of Enterobacteriaceae carriage with multiple imipenem resistant organisms (See Table 17 which shows titers (in cfu/g) of imipenem-resistant M. morganii, P. rettgeri and P. penneri from Patients 2, 4 & 5).

In addition to speciation and enumeration, multiple isolates of each organism from Patient 4 were grown overnight in 96-well trays containing a 2-fold dilution series of imipenem in order to quantitatively determine the minimum inhibitory concentration (MIC) of antibiotic. Growth of organisms was detected by light scattering at 600 nm on a SpectraMax M5e plate reader. In the clinical setting, these species are considered resistant to imipenem if they have an MIC of 1 ug/mL or greater. M. morganii isolates from pretreatment samples from Patient 4 had MICs of 2-4 ug/mL and P. penneri isolates had MICs of 4-8 ug/mL. Thus, the bacterial composition, such as but not limited to, an ethanol-treated spores administered to Patient 4 caused the clearance of 2 imipenem resistant organisms (Table 4). While this example specifically uses a spore preparation, the methods herein describe how one skilled in the art would use a more general bacterial composition to achieve the same effects. The specific example should not be viewed as a limitation of the scope of this disclosure.

Identifying the Core Ecology From the Bacterial Combination

Ten different bacterial compositions were made by the ethanol-treated spore preparation methods from 6 different donors (as described above). The spore preparations were used to treat 10 patients, each suffering from recurrent C. difficile infection. Donors were identified using the inclusion/exclusion criteria described above under provision of fecal material. None of the patients experienced a relapse of C. difficile in the 4 weeks of follow up after treatment, whereas the literature would predict that 70-80% of subjects would experience a relapse following cessation of antibiotic [Van Nood, et al, NEJM (2013)]. Thus, the ethanol-treated spore preparations derived from multiple different donors and donations showed remarkable clinical efficacy. These ethanol-treated spore preparations are a subset of the bacterial compositions described herein and the results should not be viewed as a limitation on the scope of the broader set of bacterial compositions.

To define the Core Ecology underlying the remarkable clinical efficacy of the bacterial compositions e.g. ethanol-treated spore preparations, the following analysis was carried out. The OTU composition of the spore preparation was determined by 16S-V4 rDNA sequencing and computational assignment of OTUs per Example 2. A requirement to detect at least ten sequence reads in the ethanol-treated spore preparation was set as a conservative threshold to define only OTUs that were highly unlikely to arise from errors during amplification or sequencing. Methods routinely employed by those familiar to the art of genomic-based microbiome characterization use a read relative abundance threshold of 0.005% (see e.g. Bokulich, A. et al. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10: 57-59), which would equate to ≥2 reads given the sequencing depth obtained for the samples analyzed in this example, as cut-off which is substantially lower than the ≥10 reads used in this analysis. All taxonomic and clade assignments were made for each OTU as described in Example 2. The resulting list of OTUs, clade assignments, and frequency of detection in the spore preparations are shown in Table 18. Table 18 shows OTUs detected by a minimum of ten 16S-V4 sequence reads in at least one ethanol-treated spore preparatio. OTUs that engraft in a treated patients and the percentage of patients in which they engraft are denoted, as are the clades, spore forming status, and Keystone OTU status. Starred OTUs occur in ≥80% of the ethanol preps and engraft in ≥50% of the treated patients.

Next, it was reasoned that for an OTU to be considered a member of the Core Ecology of the bacterial composition, that OTU must be shown to engraft in a patient. Engraftment is important for two reasons. First, engraftment is a sine qua non of the mechanism to reshape the microbiome and eliminate C. difficile colonization. OTUs that engraft with higher frequency are highly likely to be a component of the Core Ecology of the spore preparation or broadly speaking a set bacterial composition. Second, OTUs detected by sequencing a bacterial composition (as in Table 6 may include non-viable cells or other contaminant DNA molecules not associated with the composition. The requirement that an OTU must be shown to engraft in the patient eliminates OTUs that represent non-viable cells or contaminating sequences. Table 6 also identifies all OTUs detected in the bacterial composition that also were shown to engraft in at least one patient post-treatment. OTUs that are present in a large percentage of the bacterial composition e.g. ethanol spore preparations analyzed and that engraft in a large number of patients represent a subset of the Core Ecology that are highly likely to catalyze the shift from a dysbiotic disease ecology to a healthy microbiome.

A third lens was applied to further refine insights into the Core Ecology of the bacterial composition (e.g. spore preparation). Computational-based, network analysis has enabled the description of microbial ecologies that are present in the microbiota of a broad population of healthy individuals (see Example 5). These network ecologies are comprised of multiple OTUs, some of which are defined as Keystone OTUs. Keystone OTUs are computationally defined as described in Example 6. Keystone OTUs form a foundation to the microbially ecologies in that they are found and as such are central to the function of network ecologies in healthy subjects. Keystone OTUs associated with microbial ecologies associated with healthy subjects are often are missing or exist at reduced levels in subjects with disease. Keystone OTUs may exist in low, moderate, or high abundance in subjects. Table 6 further notes which of the OTUs in the bacterial composition e.g. spore preparation are Keystone OTUs exclusively associated with individuals that are healthy and do not harbor disease. The presence of computationally derived Keystone OTUs in the Core Ecology of the doses validates the predictive capacity of computationally derived network ecologies.

There are several important findings from this data. A relatively small number of species, 16 in total, are detected in all of the spore preparations from 6 donors and 10 donations. This is surprising because the HMP database (hmpdacc.org) describes the enormous variability of commensal species across healthy individuals. The presence of a small number of consistent OTUs lends support to the concept of a Core Ecology and Backbone Networks. The engraftment data further supports this conclusion. A regression analysis shows a significant correlation between frequency of detection in a spore preparation and frequency of engraftment in a donor: R=0.43 (p<0.001). While this may seem obvious, there is no a priori requirement that an OTU detected frequently in the bacterial composition e.g. spore preparation will or should engraft. For instance, Lutispora thermophila, a spore former found in all ten spore preparations, did not engraft in any of the patients. Bilophila wadsworthia, a gram negative anaerobe, is present in 9 of 10 donations, yet it does not engraft in any patient, indicating that it is likely a non-viable contaminant in the ethanol-treated spore preparation. Finally, it is worth noting the high preponderance of previously defined Keystone OTUs among the most frequent OTUs in the spore preparations.

These three factors—prevalence in the bacterial composition such as but not limited to a spore preparation, frequency of engraftment, and designation as a Keystone OTUs—enabled the creation of a “Core Ecology Score” (CES) to rank individual OTUs. CES was defined as follows:

40% weighting for presence of OTU in spore preparation

-   -   multiplier of 1 for presence in 1-3 spore preparations     -   multiplier of 2.5 for presence in 4-8 spore preparations     -   multiplier of 5 for presences in ≥9 spore preparations

40% weighting for engraftment in a patient

-   -   multiplier of 1 for engraftment in 1-4 patients     -   multiplier of 2.5 for engraftment in 5-6 patients     -   multiplier of 5 for engraftment in ≥7 patients

20% weighting to Keystone OTUs

-   -   multiplier of 1 for a Keystone OTU     -   multiplier of 0 for a non-Keystone OTU

Using this guide, the CES has a maximum possible score of 5 and a minimum possible score of 0.8. As an example, an OTU found in 8 of the 10 bacterial composition such as but not limited to a spore preparations that engrafted in 3 patients and was a Keystone OTU would be assigned the follow CES:

CES=(0.4×2.5)+(0.4×1)+(0.2×1)=1.6

Table 7 ranks the top 20 OTUs by CES with the further requirement that an OTU must be shown to engraft to be a considered an element of a core ecology.

Defining Efficacious Subsets of the Core Ecology

The number of organisms in the human gastrointestinal tract, as well as the diversity between healthy individuals, is indicative of the functional redundancy of a healthy gut microbiome ecology (see The Human Microbiome Consortia. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214). This redundancy makes it highly likely that subsets of the Core Ecology describe therapeutically beneficial components of the bacterial composition such as but not limited to an ethanol-treated spore preparation and that such subsets may themselves be useful compositions for populating the GI tract and for the treatment of C. difficile infection given the ecologies functional characteristics. Using the CES, individual OTUs can be prioritized for evaluation as an efficacious subset of the Core Ecology.

Another aspect of functional redundancy is that evolutionarily related organisms (i.e. those close to one another on the phylogenetic tree, e.g. those grouped into a single clade) will also be effective substitutes in the Core Ecology or a subset thereof for treating C. difficile.

To one skilled in the art, the selection of appropriate OTU subsets for testing in vitro (see Example 20 below) or in vivo (see Examples 13 or 14) is straightforward. Subsets may be selected by picking any 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 OTUs from Table 6, with a particular emphasis on those with higher CES, such as the OTUs described Table 7. In addition, using the clade relationships defined in Example 2 above and Table 1, related OTUs can be selected as substitutes for OTUs with acceptable CES values. These organisms can be cultured anaerobically in vitro using the appropriate media (selected from those described in Example 5 above), and then combined in a desired ratio. A typical experiment in the mouse C. difficile model utilizes at least 10⁴ and preferably at least 10⁵, 10⁶, 10⁷, 10⁸, 10⁹ or more than 10⁹ colony forming units of a each microbe in the composition. Variations in the culture yields may sometimes mean that organisms are combined in unequal ratios, e.g. 1:10, 1:100, 1:1,000, 1:10,000, 1:100,000, or greater than 1:100,000. What is important in these compositions is that each strain be provided in a minimum amount so that the strain's contribution to the efficacy of the Core Ecology subset can be measured. Using the principles and instructions described here, it is straightforward for one of skill in the art to make clade-based substitutions to test the efficacy of subsets of the Core Ecology. Table 18 describes the clades for each OTU detected in a spore preparation, and Table 1 describes the OTUs that can be used for substitutions based on clade relationships. Examples of network ecologies empirically screened in vivo are presented in Example 13 below.

Example 12. Presence of Network Ecologies and Keystone OTUs in Clinically Prepped Ethanol-Treated Spore Preparation and CDAD Patients Post Treatment

Network ecologies computationally determined as described in Example 5 and reported in Table 8 as being networks or subsets of networks characteristic of health states in the context of CDAD or other disease indications (Table 14a-b) are observed in the ethanol-treated spore preparation (a.k.a. the bacterial composition) and the microbiome of patients post treatment (see Example 11) indicating that they play an important role in treatment of CDAD and other indications. For each computationally determined network ecology (Table 8), we determined whether the full network or a subset of the network was observed in the microbiome of (i) each of the 10 ethanol-treated spore preparations used to treat patients with recurrent Clostridium difficile associated diarrhea; (ii) the engrafted ecology of each of the 10 patients (see Example 11); (iii) the augmented ecology of each of the 10 patients (see Example 11); or (iv) of each of the 10 patient's microbiome pretreatment. If the computationally determined networks are indeed representative of a state of health and not a disease state, one would expect that these networks would be responsible for catalyzing a shift from a disease state to a health state. This can happen either by the network ecology changing the gut environment to favor the growth of OTUs that are required to establish a health state (i.e. promoting augmentation) or by the engraftment of OTUs in the bacterial composition or both. Applicants observed that numerous computationally determined networks and/or subsets of these networks were in fact observed both in the bacterial composition used to treat the patients and the microbiota that expanded post-treatment (Table 14b). These same networks or sub-sets of networks were significantly under-represented in the patients pre-treatment. To demonstrate this, we computed the percentage of network OTUs that are found in (i) the treatment bacterial composition, (ii) the post-treatment augmented ecology, (iii) the post-treatment engrafted ecology, and (iv) the pretreatment ecology (i.e. patient microbiome prior to administration of the bacterial composition). Applicants observed across all doses of bacterial composition and patient samples that on average 46%±19%, 28%±14%, 11%±8%, and 7%±4% of the computed networks OTUs were present in the various microbiome ecologies, respectively (reported here as average±standard deviation). There was a significant difference (p<0.0001, ANOVA) between all of these percentages indicating that prior to treatment, the OTUs found in CDAD patients are significantly under-represented in the networks, and that the network OTUs are significantly over-represented in the bacterial compositions and post-treatment patient samples, affirming the predictive utility of the computational network analysis. These results in combination with those reported in Table 14b demonstrate that, prior to treatment, the patients harbored a significantly lower number of OTUs that comprised network ecologies. In contrast, the ecology of the bacterial composition, as well as the augmenting ecologies whose appearance was catalyzed by the spore population, were significantly overrepresented in patients whose CDAD resolved due to treatment.

We observed both large and small computationally determined network ecologies characteristic of states of health in the ethanol-treated spore population and the patients post treatment (Table 14a). These observed networks ranged in size from 2-15 OTUs and were comprised of OTUs that represented from 29% to 100% of the OTUs in the computationally determined network ecology. Notably, on average the network ecologies found in the ethanol-treated spore population or the patient ecologies post treatment comprised 72%±15% (average±SD) of the computationally determined network ecology again strongly indicating an important role of the computed network ecologies in catalyzing a shift in a dysbiotic disease ecology to a state of health in these patients with recurrent CDAD. Further, Keystone OTUs in the computationally determined network ecologies were frequently observed in the ethanol-treated spore preparations and in the patients' post-treatment gut ecologies. Clades representing Keystone OTUs where typically more common in the bacterial composition and post-treatment patient ecologies than in the pre-treatment dysbiotic patient ecology (Table 15).

The computed network ecologies and their respective subsets that are observed in the ethanol-treated spore preparation and the various patient ecologies post-treatment represent both complete and foundational networks (e.g., Backbone Network Ecology). Microbial therapeutics can be comprised of these network ecologies in their entirety, or they can be modified by the addition or subtraction of other OTUs or functional modalities as described in Example 7 and Example 22 to design particular phylogenetic and/or functional characteristics, including metabolic functions such as SCFA production or bile acid metabolism, into the microbial therapeutic.

Example 13. In Vivo Validation of Network Ecology Bacterial Compositions Efficacy in Clostridium Difficile Infection Prevention Mouse Model

To test the therapeutic potential of the bacterial composition such as but not limited to a spore population, a prophylactic mouse model of C. difficile infection was used (model based on Chen X, Katchar K, Goldsmith J D, Nanthakumar N, Cheknis A, Gerding D N, Kelly C P. 2008. A mouse model of Clostridium difficile-associated disease. Gastroenterology 135: 1984-1992.). Two cages of five mice each were tested for each arm of the experiment. All mice received an antibiotic cocktail consisting of 10% glucose, kanamycin (0.5 mg/ml), gentamicin (0.044 mg/ml), colistin (1062.5 U/ml), metronidazole (0.269 mg/ml), ciprofloxacin (0.156 mg/ml), ampicillin (0.1 mg/ml) and Vancomycin (0.056 mg/ml) in their drinking water on days −14 through −5 and a dose of 10 mg/kg Clindamycin by oral gavage on day −3. On day −1, test articles are spun for 5 minutes at 12,100 rcf, their supernatants' removed, and the remaining pellets are resuspended in sterile PBS, prereduced if bacterial composition is not in spore form, and delivered via oral gavage. On day 0 they were challenged by administration of approximately 4.5 log 10 cfu of C. difficile (ATCC 43255) or sterile PBS (for the Naive arm) via oral gavage. Optionally a positive control group received vancomycin from day −1 through day 3 in addition to the antibiotic protocol and C. difficile challenge specified above. Feces were collected from the cages for analysis of bacterial carriage. Mortality, weight and clinical scoring of C. difficile symptoms based upon a 0-4 scale by combining scores for Appearance (0-2 pts based on normal, hunched, piloerection, or lethargic), and Clinical Signs (0-2 points based on normal, wet tail, cold-to-the-touch, or isolation from other animals) are assessed every day from day −2 through day 6. Mean minimum weight relative to day −1 and mean maximum clinical score where a death is assigned a clinical score of 4 as well as average cumulative mortality are calculated. Reduced mortality, increased mean minimum weight relative to day −1, and reduced mean maximum clinical score with death assigned to a score of 4 relative to the vehicle control are used to assess the success of the test article.

Table 16 reports results for 15 experiments of the prophylactic mouse model of C. difficile infection. In the 15 experiments, 157 of the arms tested network ecologies, with 86 distinct networks ecologies tested (Table 17). Of those 157 arms, 136 of the arms and 73 of the networks performed better than the respective experiment's vehicle control arm by at least one of the following metrics: cumulative mortality, mean minimum relative weight, and mean maximum clinical score. Examples of efficacious networks include but are not limited to networks N1979 as tested in SP-361 which had 0% cumulative mortality, 0.97 mean minimum relative weight, and 0 mean maximum clinical score or N2007 which had 10% cumulative mortality, 0.91 mean minimum relative weight, and 0.9 mean maximum clinical score with both networks compared to the vehicle control in SP-361 which had 30% cumulative mortality, 0.88 mean minimum relative weight, and 2.4 mean maximum clinical score. In SP-376, N1962 had no cumulative mortality, mean maximum clinical scores of 0 at both target doses tested with mean minimum relative weights of 0.98 and 0.95 for target doses of 1e8 and 1e7 CFU/OTU/mouse respectively. These results confirm that bacterial compositions comprising bacteria identified from computationally determined networks or subsets of these determined networks have utility and efficacy in the mouse model.

Example 14. In Vivo Validation of Network Ecology Bacterial Composition Efficacy in Prophylactic and Relapse Prevention Hamster Model

Previous studies with hamsters using toxigenic and nontoxigenic strains of C. difficile demonstrated the utility of the hamster model in examining relapse post antibiotic treatment and the effects of prophylaxis treatments with cecal flora in C. difficile infection (Wilson et al. 1981, Wilson et al. 1983, Borriello et al. 1985) and more broadly in gastrointestinal infectious disease. To demonstrate prophylactic use of ethanol-treated spores and ethanol treated, gradient-purified spores to ameliorate C. difficile infection, the following hamster model was used. In the prophylactic model, Clindamycin (10 mg/kg s.c.) was given on day −5, the test article or control was administered on day −3, and C. difficile challenge occurred on day 0. In the positive control arm, vancomycin was then administered on day 1-5 (and vehicle control was delivered on day −3). Feces were collected on day −5, −4, −1, 1, 3, 5, 7, 9 and fecal samples were assessed for pathogen carriage and reduction by microbiological methods. 16S sequencing approaches or other methods could also be utilized by one skilled in the art. Mortality was assessed multiple times per day through 21 days post C. difficile challenge. The percentage survival curves showed that ethanol-treated spores and ethanol treated, gradient-purified spores better protected the hamsters compared to the Vancomycin control, and vehicle control.

FIG. 9 shows a prophylaxis model with the ethanol-treated spore preparation and the ethanol treated, gradient-purified spore preparation. In the relapse prevention model, hamsters were challenged with toxigenic C. difficile strains on day 0, and treated with clindamycin by oral gavage on day 1, and vancomycin was dosed on days 2-6. Test or control treatment was then administered on day 7, 8, and 9. The groups of hamsters for each arm consisted of 8 hamsters per group. Fecal material was collected on day −1, 1, 3, 5, 7, 10 and 13 and hamster mortality was assessed throughout. Survival curves were used to assess the efficacy of the test articles, e.g., ethanol treated or ethanol treated, gradient purified spores versus the control treatment in preventing hamster death. The survival curves demonstrated maximum efficacy for the ethanol treated, gradient-purified spores followed by the ethanol-treated spores. Both treatments improved survival percentage over vancomycin treatment.

Also in the relapse prevention model, the efficacy of a bacterial community of pure cultures, N1962, was tested. The survival curves demonstrate protection against relapse by N1962 relative to the vancomycin control treatment.

FIG. 10 shows a relapse prevention model with ethanol-treated spores and ethanol treated, gradient purified spores. In particular, it shows an in vivo hamster Clostridium difficile relapse prevention model to validate efficacy of ethanol-treated spores and ethanol treated, gradient purified spores.

FIG. 11 shows a relapse prevention model with a bacterial community. In particular, it shows an in vivo hamster Clostridium difficile relapse prevention model to validate efficacy of network ecology bacterial composition.

Example 15. Derivation of Functional Profile of Individual Microbial OTUs or Consortia of OTUs Representing Specific Network Ecologies

To generate a functional profile of an OTU, or consortium of OTUs one can leverage multiple-omic data types. These include, but are not limited to functional prediction based on 16S rRNA sequence, functional annotation of metagenomic or full-genome sequences, transcriptomics, and metabolomics. A consortium of OTUs of interest can be defined using numerous criteria including but not limited to: (i) a computationally derived network of OTUs based on the analysis of samples that represent states of health and disease such as those delineated in Example 5 and reported in Table 8, (ii) a consortia of OTUs that are identified in an individual sample or group of samples using either a 16S-based, metagenomic-based, or microbiological-based methods such as delineated in Examples 3, 4 and 16, and (iii) a list of OTUs derived from the assessment of literature.

For 16S rRNA sequences, phylogenetic investigation of communities by reconstruction of unobserved states, also known as PICRUSt (Langille M G I, Zaneveld J, Caporaso J G, McDonald D, Knights D, Reyes J A, Clemente J C, Burkepile D E, Vega Thurber R L, Knight R, et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol.), enables the prediction of a functional metabolic pathway of an OTU or a consortium of OTUs based on the KEGG database of reference functional pathways and functional ontologies (Kyoto Encyclopedia of Genes and Genomes; genome.jp/kegg/). PICRUSt matches the taxonomic annotation of a single 16S sequence read with a reference functional annotation of a genome sequence for a given OTU or set of OTUs. From these reference genome annotations, a functional annotation is assigned to each OTU. PICRUSt is composed of two high-level workflows: gene content inference and metagenome inference. The gene content inference produces gene content predictions for a set of reference OTUs as well as copy number predictions. The metagenome inference then uses these inputs and an OTU table that defines the OTUs in a sample and their relative abundances to then infer the functional metabolic profile of the OTUs in the OTU table. In an alternative, but related method, one can lookup for all of the OTUs in a consortia the OTU taxonomic identifications in a functional reference database such as IMG (http://img.jgi.doe.gov) and then derive a functional annotation of the network by concatenating the database's metabolic pathway maps (e.g. KEGG Pathway Orthology in case of IMG) for each of the OTUs in the consortia (see below for specific example).

To generate functional annotation from metagenomic or whole genome shotgun sequence data, reads are first clustered and then representative reads are annotated. Sequence annotation is then performed as described in Example 1, with the additional step that sequences are either clustered or assembled prior to annotation. Following sequence characterization as described above using a technology such as but not limited to Illumina, sequence reads are demultiplexed using the indexing barcodes. Following demultiplexing sequence reads are clustered using a rapid clustering algorithm such as but not limited to UCLUST (drive5.com/usearch/manual/uclust algo.html) or hash-based methods such VICUNA (Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J. Lennon, Joshua Z. Levin, James Qu, Elizabeth M. Ryan, Michael C. Zody, and Matthew R. Henn. 2012. De novo assembly of highly diverse viral populations. BMC Genomics 13:475). Following clustering a representative read for each cluster is identified and analyzed as described above in Example 2 “Primary Read Annotation”. The result of the primary annotation is then applied to all reads in a given cluster. In another embodiment, metagenomic sequences are first assembled into contigs and then these assembled contigs are annotated using methods familiar to one with ordinary skill in the art of genome assembly and annotation. Platforms such as but not limited to MetAMOS (TJ. Treangen et al. 2013 Geneome Biology 14:R2), and HUMAaN (Abubucker S, Segata N, Goll J, Schubert A M, Izard J, Cantarel B L, Rodriguez-Mueller B, Zucker J, Thiagaraj an M, Henrissat B, et al. 2012. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome ed. J. A. Eisen. PLoS Computational Biology 8: e1002358) are suitable for analysis of metagenomic data sets using the methods described above. Tools such as MetAMOS are also suitable for the generation of a functional annotation of complete genome sequence assembled from the sample or obtained from a reference genome database such as but not limited to NCBI's genome database (ncbi.nlm.nih.gov/genome). In all cases, functional pathways are derived from the sequence read annotations based on the mapping of the sequence annotations to a functional database, such as but not limited to KEGG (genome.jp/kegg), Biocyc (biocyc.org), IMG (img.jgi.doe.gov), MetaCyc (metacyc.org), or Reactome (reactome.org). Various tools are available for this task that are familiar to one with ordinary skill in the art including, but not limited to, The HMP Unified Metabolic Analysis Network (HUMAnN) (Abubucker S, Segata N, Goll J, Schubert A M, Izard J, Cantarel B L, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, et al. 2012. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome ed. J.A. Eisen. PLoS Computational Biology 8: e1002358). The HUMAnN software recovers the presence, absence, and abundance of microbial gene families and pathways from metagenomic data. Cleaned short DNA reads are aligned to the KEGG Orthology (or any other characterized sequence database with functional annotation assigned to genetic sequences) using accelerated translated BLAST. Gene family abundances are calculated as weighted sums of the alignments from each read, normalized by gene length and alignment quality. Pathway reconstruction is performed using a maximum parsimony approach followed by taxonomic limitation (to remove false positive pathway identifications) and gap filling (to account for rare genes in abundant pathways). The resulting output is a set of matrices of pathway coverages (presence/absence) and abundances, as analyzed here for the seven primary body sites of the Human Microbiome Project.

Transcriptomic or RNA-Seq data are also a means to generate a functional profile of a sample (Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63). Briefly, long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors appropriate to the sequencing technology being used for downstream sequencing are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. The resulting sequence reads are aligned with the reference genome or transcriptome and annotated and mapped to functional pathways as described above. Reads are categorized as three types: exonic reads, junction reads and poly(A) end-reads. These three types of reads in combination with the gene annotation are used to generate a base-resolution expression profile for each gene.

In yet another method to generate a metabolic profile of a microbial ecology, characterization of metabolites produced by the ecology are analyzed in tissues or fluids. Samples can include, without limitation, blood, urine, serum, feces, ileal fluid, gastric fluid, pulmonary aspirates, tissue culture fluid, or bacterial culture supernatants. Both targeted and untargeted methods can be utilized for metabolomics analysis (Patti G J, Yanes O, Siuzdak G. 2012. Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 13: 263-269.). Metabolomic methods utilize LC/MS-based technologies to generate a metabolite profile of sample. In the triple quadrupole (QqQ)-based targeted metabolomic workflow, standard compounds for the metabolites of interest are first used to set up selected reaction monitoring methods. Here, optimal instrument voltages are determined and response curves are generated using reference standards for absolute quantification. After the targeted methods have been established on the basis of standard metabolites, metabolites are extracted from the sample using methods familiar to one with ordinary skill in the art. Extraction methods can include liquid:liquid extraction using organic solvents or two-phase aqueous methods, solid phase extraction using hydrophobic or ion exchange resins, filtrations to remove solid contaminants, centrifugation or other means of clarification, and counter-current techniques. The data output provides quantification only of those metabolites for which standards are available. In the untargeted metabolomic workflow, extracted metabolites are first iseparated by liquid chromatography followed by mass spectrometry (LC/MS). After data acquisition, the results are processed by using bioinformatic software such as XCMS to perform nonlinear retention time alignment and identify peaks that are changing between the groups of related samples. The m/z values for the peaks of interest are searched in a metabolite databases to obtain putative identifications. Putative identifications are then confirmed by comparing tandem mass spectrometry (MS/MS) data and retention time data to that of standard compounds. The untargeted workflow is global in scope and outputs data related to comprehensive cellular metabolism.

Applicants generated a functional profile for all of the computationally determined network ecologies delineated in Table 8 and Table 14a that were derived using the methods outlined in Example 5. Table 18 and Table 21 provide written description of the corresponding functional network ecologies respectively. For each network, applicants generated a functional metabolic profile by concatenating the KEGG Orthology Pathways for each OTU available in the IMG functional database (img.jgi.doe.gov). The taxonomic annotations of each OTU in the network were mapped to the taxon_display_names in the IMG database. For each taxon_display_name the taxon_iod with the best 16S sequence match to the 16S sequence of the OTU in the computed network ecology was selected (best match based on expectation value and an alignment score). The functional annotation for each OTU in the network was then derived from IMG's KEGG Orthology Pathway (i.e. ko_id) for the given taxon_iod. KEGG Orthology Pathways (KO) for all the OTUs in the network were concatenated and then the list was made unique to generate a non-redundant functional profile of the network. In another embodiment, the ko_id list is not made unique and the functional profile of the network is defined based on the relative abundances of the ko_ids not just their presence or absence. It is with the level of ordinary skill using the aforementioned disclosure to construct functional network ecologies that substitute the exemplified OTUs with equivalent OTUs that harbor the orthologous KEGG Orthology Pathways. Such substitiutions are contemplated to be within the scope of the present invention, either literally or as an equivalent to the claimed invention as determined by determined by a court of competent jurisdiction.

Each functional network ecology was scored for its ability to metabolize bile acids and to produce short chain fatty acids (SCFAs). As described above, both bile acid metabolism and the production of SCFAs by bacterial ecologies plays an important role in human health. Specifically, applicants subsetted the KEGG Orthology Pathways computed for each network ecology to those described to be involved in secondary bile acid biosynthesis, butryrate (a.k.a. butanoate) metabolism, propionate (a.k.a. propanoate) metabolism, or pyruvate metabolism (leads to production of acetate). We identified and ranked network ecologies for their capacity to metabolize bile acid and produce SCFAs by defining a bile acid and SCFA functional score (F-Score) that defines a network ecologies' capacity to perform these two important metabolic roles. The F-score is defined by the total number of KEGG Orthology Pathways in a given network that mapped to secondary bile acid biosynthesis, a butyrate metabolism, a propionate metabolism, or a pyruvate metabolism (Table 18). A functional translation of the KEGG Orthology Pathways (i.e., KO numbers) and their respective metabolic ontology classification is provided in Table 19 as reference. Significantly, as shown in Table 18, there are only two computed network ecologies that did not harbor at least one pathway related to secondary bile acid biosynthesis, butyrate metabolism, propionate metabolism, or a pyruvate metabolism, suggesting both likely importance of these pathways to the metabolism of a large number of gastrointestinal ecologies, and the importance of these pathways to catalyzing a shift from a disease to a health state in the example cases of CDAD and Type 2 Diabetes.

Example 16. Use of Biolog Assay to Generate a Nutrient Utilization Functional Profile of an OTU or Consortium of OTU

Metabolic capabilities of individual organisms or a consortia of organisms can be determined using Biolog technology in which metabolic activity is detected by measurement of NADH production using a redox sensitive dye. Carbon source or other metabolic capabilities of a single species can be determined, as described below. Carbon source utilization of an ecology or network can also be assessed using the same methods.

A screen was performed to test the ability of Clostridium difficile and potential competitor species to utilize a panel of 190 different carbon sources. The screen was carried out using PM1 and PM2 MicroPlates (Biolog #12111, #12112), IF-0a base media (Biolog #72268) and Biolog Redox Dye Mix D (Biolog #74224). For each strain, a 1 uL aliquot from −80° C. glycerol stock was streaked out for single colonies to solid Brucella Blood Agar plates (BBA) (Anaerobe Systems #AS-111) and incubated anaerobically at 37° C. for 24 hr. A single colony was then re-streaked to a BBA plate and incubated anaerobically at 37° C. for 24 hr. The MicroPlates were pre-reduced by incubating for at least 24 hr in a hydrogen free anaerobic environment before use. All liquid media and supplements used were pre-reduced by placing them in an anaerobic chamber with loose lids for at least 24 hr before use. Alternatively, combinations of bacteria can also be tested.

The base media for inoculation was prepared by adding 0.029 mL of 1M potassium ferricyanide to 0.240 mL of Dye Mix D followed by addition of 19.7 mL of IF-0a, 4 mL sterile water and 0.024 mL 0.5 mM menadione. For some species, the concentrations of potassium ferricyanide and menadione were adjusted to achieve the optimal redox balance or to test multiple redox conditions. Potassium ferricyanide was tested at a final concentration of 0.38, 0.12, 0.038 and 0.06 mM. Menadione was tested at a final concentration of 0.5, 0.16 and 0.05 μM. In total, this yields 9 redox conditions for testing. Reduction of the tetrazolium dye that forms the basis for the endpoint measurement was sensitive to the redox state of each bacterial culture, and thus to the ratio of menadione to potassium ferricyanide. It was therefore important to test various ratios for each bacterial isolate and was also important in some cases to test a species at multiple menadione/potassium ferricyanide ratios in order to detect all conditions in which a possible nutrient utilization was detectable. Some species were tested beyond the 20 hr time point to detect all conditions resulting in a positive result. In these cases plates were read at 20, 44 or 96 hr.

Using a sterile, 1 μL microbiological loop, a loopful of biomass was scraped from the BBA plate and resuspended in the base media by vortexing. The OD was adjusted to 0.1 at 600 nm using a SpectraMax M5 plate reader. The bacterial suspension was then aliquoted into each well of the PM1 and PM2 plates (100 μL per well). The plates were incubated at 37° C. for 20 hr in a rectangular anaerobic jar (Mitsubishi) with 3 anaerobic, hydrogen-free gas packs (Mitsubishi AnaeroPack). After 20 hr, OD at 550 nm was read using a SpectraMax M5 plate reader. Wells were scored as a weak hit if the value was 1.5× above the negative control well, and a strong hit if the value was 2× above the negative control well. The results are shown in the Table in FIG. 4.

The following list of nutrient sources were tested: L-Arabinose, N-Acetyl-D-Glucosamine, D-Saccharic Acid, SuccinicAcid, D-Galactose, L-AsparticAcid, L-Proline, D-Alanine, D-Trehalose, D-Mannose, Dulcitol, D-Serine, D-Sorbitol, Glycerol, L-Fucose, D-Glucuronic Acid, D-Gluconic Acid, D, L-alpha-Glycerol-Phosphate, D-Xylose, L-Lactic Acid, Formic Acid, D-Mannitol, L-Glutamic Acid, D-Glucose-6-Phosphate, D-Galactonic Acid-gamma-Lactone, D,L-Malic Acid, D-Ribose, Tween 20, L-Rhamnose, D-Fructose, Acetic Acid, alpha-D-Glucose, Maltose, D-Mellibiose, Thymidine, L-Asparagine, D-Aspartic Acid, D-Glucosaminic Acid, 1,2-Propanediol, Tween 40, alpha-Keto-Glutaric Acid, alpha-Keto-ButyricAcid, alpha-Methyl-D-Galactoside, alpha-D-Lactose, Lactulose, Sucrose, Uridine, L-Glutamine, M-Tartaric Acid, D-Glucose-1-Phosphate, D-Fructose-6-Phosphate, Tween 80, alpha-Hydroxy-Glutaric-gamma-lactone, alpha-Hydroxy Butyric Acid, beta-Methyl-D-Glucoside, Adonitol, Maltotriose, 2-Deoxy Adenosine, Adenosine, Glycyl-L-Aspartic Acid, Citric Acid, M-Inositol, D-Threonine, Fumaric Acid, Bromo Succinic Acid, Propionic Acid, Mucic Acid, Glycolic Acid, Glyoxylic Acid, D-Cellobiose, Inosine, Glycyl-L-Glutamic Acid, Tricarballylic Acid,L-Serine, L-Threonine, L-Alanine, L-Alanyl-Glycine, Acetoacetic Acid, N-Acetyl-beta-D-Mannosamine, Mono Methyl Succinate, Methyl Pyruvate, D-Malic Acid, L-Malic Acid,Glycyl-L-Proline, p-Hydroxy Phenyl Acetic Acid, m-Hydroxy Phenyl Acetic Acid, Tyramine, D-Psicose, L-Lyxose, Glucuronamide, Pyruvic Acid, L-Galactonic Acid-gamma-Lactone,D-Galacturonic Acid,Pheylethyl-amine,2-aminoethanol, Chondroitin Sulfate C, alpha-Cyclodextrin, beta-Cyclodextrin, gamma-Cyclodextrin, Dextrin, Gelatin, Glycogen, Inulin, Laminarin, Mannan, Pectin, N-Acetyl-D-Galactosamine, N-Acetyl-Neuramic Acid, beta-D-Allose, Amygdalin, D-Arabinose, D-Arabitol, L-Arabitol, Arbutin, 2-Deoxy-D-Ribose, I-Erythritol, D-Fucose, 3-0-beta-D-Galacto-pyranosyl-D-Arabinose, Gentibiose, L-Glucose, Lactitol, D-Melezitose, Maltitol, alpha-Methyl-D-Glucoside, beta-Methyl-D-Galactoside, 3-Methyl Glucose, beta-Methyl-D-GlucoronicAcid, alpha-Methyl-D-Mannoside, beta-Metyl-D-Xyloside, Palatinose, D-Raffinose, Salicin, Sedoheptulosan, L-Sorbose, Stachyose, D-Tagatose, Turanose, Xylitol, N-Acetyl-D-Glucosaminitol, gamma-Amino Butyric Acid, delta-Amino Valeric Acid, Butyric Acid, Capric Acid, Caproic Acid, Citraconic Acid, Citramalic Acid, D-Glucosamine, 2-Hydroxy Benzoic Acid, 4-Hydroxy Benzoic Acid, beta-Hydroxy Butyric Acid, gamma-Hydroxy Butyric Acid, alpha-Keto Valeric Acid, Itaconic Acid, 5-Keto-D-Gluconic Acid, D-Lactic Acid Methyl Ester, Malonic Acid, Melibionic Acid, Oxalic Acid, Oxalomalic Acid, Quinic Acid, D-Ribino-1,4-Lacton, Sebacic Acid, Sorbic Acid, Succinamic Acid, D-Tartaric Acid, L-Tartaric Acid, Acetamide, L-Alaninamide, N-Acetyl-L-Glutamic Acid, L-Arginine, Glycine, L-Histidine, L-Homserine, Hydroxy-L-Proline, L-Isoleucine, L-Leucine, L-Lysine, L-Methionine, L-Ornithine, L-Phenylalanine, L-Pyroglutamic Acid, L-Valine, D,L-Carnithine, Sec-Butylamine, D,L-Octopamine, Putrescine, Dihydroxy Acetone, 2,3-Butanediol, 2,3-Butanone, 3-Hydroxy 2-Butanone.

Additionally, one of skill in the art could design nutrient utilization assays for a broader set of nutrients using the methods described above including complex polysaccharides or prebiotics.

A similar screen can be performed to test the utilization of vitamins, amino acids, or cofactors. In these instances, Biolog MicroPlates for screening of vitamins, amino acids or cofactors that are of interest would be used in place of the PM1 and PM2 plates, for example PMS. Table 2 contains a list of representative vitamins, minerals, and cofactors. For each strain tested, a universal carbon source such as glucose will be used as a positive control to demonstrate reduction of the tetrazolium dye under the specific conditions of the assay.

Example 17. In Vitro Screening of Microbes for 7-Alphadehydroxylase Activity

Cultures of individual microbes are grown overnight and frozen for later use as described according to Example 9. The sodium salts of CA, CDCA, GCA, GCDCA, TCA, and TCDCA (Sigma) are obtained and prepared as aqueous stock solutions. For initial screening to define organisms capable of 7-alphadehydroxylation reactions, growth media are prepared containing 0.4 mM of each bile salt. Cultures are inoculated from a 1:100 dilution of the frozen stock into the media and grown in an anaerobic chamber for 24-48 hours, or until the culture is turbid. Two mL of culture is acidified by the addition of 1 mL of 2N HCl and 100 ug of 23-nordeoxycholic acid (Steraloids) as an internal reference standard. The acidified mixture is extracted twice with 6 mL of diethyl ether. The organic extracts are combined and then evaporated and derivatized to methyl esters with diazomethane. Gas chromatography is performed on a 7 ft (ca. 2 m) 3% OV-1 column at 260° C. and a 3% OV-17 column at 250° C. after trimethylsilylation of the methylated bile acids with Tri-Sil (Pierce, Rockford, Ill.). The retention times of the silylated bile acids are compared with those of reference products representing CA, CDCA, DCA and LCA.

For strains showing 7-alphadehydroxylase activity, a kinetic assessment is performed by harvesting a growing culture of each organisms of interest, washing and resuspending in fresh media at a concentration of between 108 to 1010 cfu/mL. The sodium salts of CA, CDCA, GCA, GCDCA, TCA, and TCDCA are then added at 0.5 to 5 mM and the resulting culture is sampled at 1, 2, 4 and 8 hours. The sample is analyzed as described above to find organisms with maximal activity. Highly active strains are selected for further incorporation into microbial compositions that exhibit maximal 7-alphadehydroxylase activity.

Example 18. In Vitro Screening of Microbes for Bile Salt Hydrolase Activity

Cultures of individual microbes are grown overnight and frozen for later use as described according to Example 9. The sodium salts of GCA, GCDCA, TCA, and TCDCA (Sigma) are obtained and prepared as aqueous stock solutions. Overnight, actively growing cultures are combined with 0.5 to 5 mM of conjugated bile acid and allowed to incubate for 24-48 hours. To analyze cultures, 0.5 mL of culture is first centrifuged at 3,000×g for 10 min to remove the bacteria, and is then acidified with 5 uL of 6 N HCl. This acidified supernatant is combined with an equal volume of methanol containing 4 mM of 23-nordeoxycholic as an internal standard. The samples are vortexed for at least 2 min and clarified by centrifugation at 1000×g for 15 min. Samples are filtered through a 0.2 um filter prior to HPLC analysis according to the method described by Jones et al2003 J Med Sci 23: 277-80. Briefly, the isocratic method is performed on a reversed-phase C-18 column (LiChrosorb RP-18, 5 m, 250×4.6 mm from HiChrom, Novato, Calif., USA). Acetate buffer is prepared daily with 0.5 M sodium acetate, adjusted to pH 4.3 with o-phosphoric acid, and filtered through a 0.22 m filter. The flow is 1.0 mL/min and the detection is performed at 205 nm. The injection loop is set to 20 uL.

For strains showing bile salt hydrolase activity, a kinetic assessment is performed by harvesting a growing culture of each organisms of interest, washing and resuspending in fresh media at a concentration of between 108 to 1010 cfu/mL. The sodium salts of GCA, GCDCA, TCA, and TCDCA are then added at 0.5 to 5 mM and the resulting culture is sampled at 1, 2, 4 and 8 hours. The sample is analyzed by HPLC as described above to find organisms with maximal activity. Highly active strains are selected for further incorporation into microbial compositions that exhibit maximal bile salt hydrolase activity.

Example 19. In vitro Screening of Microbial Communities for 7-alpha-dehydroxylase Activity

Measurement of the conversion of 7-alpha-hydroxyl bile salts (primary bile salts) to 7-dehydroxy-bile salts (secondary bile salts) by single bacterial strains or bacterial communities is determined in an in vitro assay, and can be used to screen a library of organisms, whole communities or subsets of communities using limiting dilutions to identify simpler compositions. Communities to be studies include cecal or fecal communities from animals with altered gastrointestinal microbiota due to antibiotics, diet, genetics, enterohepatic metabolism, or other experimental perturbations that cause GI alterations, or from human fecal samples from healthy individuals or those with altered gastrointestinal microbiomes due to antibiotics, diet, enterohepatic metabolism dysfunction, metabolic dysfunction, or gastrointestinal infection. Dilutions or subsets of these communities (such as could be generated by selective culturing for of the whole community to enrich for aerobes, anaerobes, Gram positives, Gram negatives, spore formers or using other microbiological selections known to one skilled in the art) can be utilized to identify a group of organisms required for a particular multi-step conversion.

To assay 7-alpha-dehydroxylation activity in vitro, an enzymatic assay is established to quantify the amount of 7-alphahydroxy bile acid in a sample. Recombinant 7-alpha-hydroxysteroid dehydrogenase (7-alpha-HSDH) from E. coli (MyBiosource.com) is an enzyme that oxidizes the 7-hydroxy group to a ketone and simultaneously reduces NAD+ to NADH+H+. The production of NADH is monitored at 340 nm using the extinction co-efficient of 6.2×103 M-1 cm-1.

A community of microbes is prepared according to Example 9 or, alternatively a preparation of cecal or fecal bacteria from mice or from human feces or a dilution thereof, or an enriched community thereof, can be tested after being washed 5 times to remove bile acids from the matrix. To the initial sample, a mixture of one or more primary bile acids including but not limited to CA, CDCA or any of their taurine or glycine conjugates is added to a final total concentration of 0.5-5 mM. An initial 100 uL aliquot is removed and heated at 55° C. for 15 min to quench further enzymatic activity. The bacterial composition is then incubated under anaerobic conditions at 37° C., and aliquots are removed sequentially after 30 min, 1 hour, 2 hours, 4 and 8 hours and heated as per above. An assay mix is prepared by combining 0.9 mL glycine-NaOH buffer pH 9.5, 50 uL of 53 mM NAD+ (Sigma), and 20 uL of freshly prepared 7-alpha-HSDH (4 mg/mL in distilled water). 80 uL of assay mix is combined with 20 uL of each aliquot in a 96-well microtiter plate and incubated at 37° C. on a SpectraMax m5 plate reader, monitoring A340. The incubation is allowed to proceed until the A340 value achieves its maximum. Total 7-alpha-hydroxyl bile acid is determined using the extinction coefficient for NADH. Changes due to dehydroxylation by the bacterial composition are calculated by subtracting the final value at any timepoint from the initial value.

Microbial communities of interest can be further fractionated using methods described in Example 9.

Example 20. In Vitro Evaluation of Mixed Microbial Cultures for Bile Acid Metabolism

Candidates strains identified in Examples 17, 18 and 19 above are tested using the methods defined for bile salt hydrolase activity and 7-alphadehydroxylase activity are combined in communities to evaluate synergies among strains and define ecologies for further testing in animal models. Synergies include: i) the potential for more rapid conversion from conjugated primary bile salts to unconjugated, dehydryoxylated bile acids; ii) the potential for a broader range of products than determined by the additive combination of activities; iii) equivalent activity at a lower concentration (cfu) of the individual strains. Combinations exhibiting such synergies are particularly favored for subsequent in vivo testing. Another important function of a community is to remove endproducts of a microbial conversion so as to avoid inhibition of growth through product accumulation. For bile acid conversion, communities can optionally include organisms capable of degrading taurine, using it both as a carbon and nitrogen source and using the sulfonic acid group as an electron acceptor in fermentation.

Example 21. Combinations of Bacterial Compositions For SCFA Production Under Variable Conditions

Combinations of synergistic bacterial compositions may be selected such that the composition is capable of producing SCFA under a wide range of in vitro conditions when the entire mixture is tested together. That is, a combination of bacterial compositions comprises multiple pairs of organisms that, together with a complex carbon source, are capable of synthesizing SCFA. Combinations may be constructed that are capable of producing a given set of SCFAs, for example butyrate and proprionate, but not acetate, or that produce butyrate, proprionate and acetate, but that the acetate is then used by another organism as a carbon source. A number of specific combinations of final SCFAs may be generated by communities designed by one skilled in the art. Construction of bacterial combinations follows the protocol described in Example 9.

Example 22. De Novo Design of Network Ecologies with Specific Functional Properties

The role of the microbiome in mediating and influencing human metabolic function is well established. Microbes produce secondary bile acids (as example, Louis P, Flint H J. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 294: 1-8.), short chain fatty acids (for example, Smith P M et al. 2013 Science. The microbial metabolites, short-chain fatty acid regulate colonic Treg cell homeostasis 341: 569-73) as well as numerous other functional metabolites that influence immunity and metabolic health of the human host.

To identify consortia of microbes suitable for the use as therapeutics, to influence host metabolic functions, and to treat microbial dysbiosis one can computationally derive in silico network ecologies that possess specific metabolic functions such as, but not limited to, a single or multiple metabolic nodes in the functional pathways involved in secondary bile acid biosynthesis (FIG. 12), butyrate metabolism (FIG. 13), propionate metabolism (FIG. 14), or pyruvate metabolism (FIG. 15). As additional examples, network ecologies can be in silico designed to target host genes involved in important host:microbe innate and adaptive immune responses through targets such as the Toll-like receptors (TLRs) and nucleotide-binding oligomerization domains (NOD) (Saleh M, Trinchieri G. 2011. Innate immune mechanisms of colitis and colitis-associated colorectal cancer. Nat Rev Immunol 11: 9-20. and Knight P, Campbell B J, Rhodes J M. 2008. Host-bacteria interaction in inflammatory bowel disease. Br Med Bull 88: 95-113.). In addition, the functional pathways to target for in silico network ecology design can be empirically defined by comparing the microbiomes of samples derived from different phenotypes such as but not limited to a state of disease and a state of health. For example, one can compare the microbiome and corresponding metabolic functional profile of individuals with and without insulin resistance. Vrieze et al. have shown that treatment with vancomycin can reduce the diversity of the microbiome and result in a small, but statistically significant change in peripheral insulin sensitivity. Similar changes are not observed following amoxicillin treatment (Vrieze, A et al., 2013, J Hepatol. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity dx.doi.org/10.1016/j.jhep.2013.11.034). Decreased insulin sensitivity was associated with a decrease in the presence of secondary bile acids DCA, LCA and iso-LCA and an increase in primary bile acids CA and CDCA increased. In another example, Applicants can compare the microbiome and metabolomic profile of healthy individuals to those with CDAD disease. In yet another example, Applicants can compare the microbiome and metabolomic profile of healthy individuals to those that harbor IBD, IBS, Ulcerative Colitis, Crohn's Disease, Type-2-Diabetes, or Type-1-Diabetes.

For both CDAD and insulin resistance, Applicants can define the functional metabolic profile of the respective disease and health microbiomes using the 16S and metagenomic genomic methods outlined in Example 15. In another embodiment, Applicants can use the transcriptomic and metabolomic methods outlined in Example 15. In another embodiment we use functional metabolic information garnered from the literature and derived from functional screens such as but not limited to Biolog MicroPlates (see Example 16). From these profiles, Applicants can generate a metabolic function matrix for both the disease state and the health state. This matrix is comprised of columns of OTUs and rows of KEGG Orthology Pathways delineated as described in Example 15. A metabolic function matrix can be generated for both the disease state and the health state. From these disease and health matrices, Applicants can compute a delta-function matrix (i.e. difference matrix) that defines the OTUs, the relative abundance of the metabolic pathways they harbor, and the difference in the relative abundance between the disease and health state. In another embodiment, the relative abundances are discretized to be a binary, ternary, or quaternary factor. This delta-function matrix defines the differences in the microbiome distinguishing the disease state from the health state.

One can then design a network ecology with the desired functional characteristics described by the delta-function matrix. In one embodiment, one can use a greedy algorithm to optimize for the most parsimonious solution to the delta-function matrix. One can design towards (i.e. select) the minimal number of OTUs to capture the full breadth of KEGG Orthology Pathways that are represented in the health state. In short, the greedy algorithm repetitively samples the OTUs spanning the greatest number of health associated KEGGs until the desired breath of KEGGs is obtained to define a functional network ecology comprised of specific OTUs. In another embodiment, one can optimize the greedy algorithm to weigh OTUs that are from specific phylogenetic clades. In another embodiment, one can start with the computationally derived network ecologies derived using the methods defined in Example 5 to both seed and constrain the greedy algorithm to return functional network ecologies that embody the co-occurrence relationships that exist between OTUs. Microbial therapeutic compositions comprised of the OTUs of the computed network ecologies are constructed using the methods defined in Example 9. In one embodiment, constraints around network ecologies are defined by networks found in specific individuals. In another embodiment, strains of each OTU that are used for construction preferentially are selected from strains isolated from the same individual since these strains are evolutionary co-evolved and have an increased likelihood of functional synergy.

In another embodiment, Applicants computationally defined in silico a network ecology with the explicit capacity to produce butyrate. In this embodiment, Applicants defined the health state in terms of the metabolic pathways and associated gene products required for the metabolism of non-digestable carbohydrates via fermentation by colonic bacteria and by the gene products leading from mono- and di-saccharides and simple substrates such as acetate and lactate to butyrate (FIGS. 12-15). We then used the IMG functional database (http://img.jgi.doe.gov) of OTU KEGG Orthology Pathways (i.e. ko_id) to generate a metabolic function matrix comprised of columns of OTUs and rows of KEGG Orthology Pathways delineated as described in Example 15. This matrix was restricted to OTUs known to reside in the gastrointestinal tract. From this metabolic function matrix we used the greedy algorithm described above to design network ecologies capable of butyrate production.

Example 23. Identification of Organisms Harboring butyryl-CoA: Acetate CoA Transferase Genes

A panel of putative butyrate forming bacteria can be screened for the presence of butyryl-CoA: acetate CoA transferase genes to define candidates for SCFA production. Bacteria are scraped from isolated colonies on agar plates or from liquid culture (media selected from Example 9) and subjected to DNA isolation in 96-well plates. 1 μl of microbial culture or an amount of a bacterial colony approximately 1 μL in volume is added to 9 μl of Lysis Buffer (25 mM NaOH, 0.2 mM EDTA) in each well of a 96 well, thin walled PCR plate, sealed with an adhesive seal, and the mixture is incubated at 95° C. for 30 minutes. Subsequently, the samples are cooled to 4° C. and neutralized by the addition of 10 μl of Neutralization Buffer (40 mM Tris-HCl) and then diluted 10-fold in Elution Buffer (10 mM Tris-HCl), at which point the genomic DNA is suitable for use in downstream amplifications such as PCR amplification. Alternatively, genomic DNA is extracted from pure microbial cultures using commercially available kits such as the Mo Bio Ultraclean® Microbial DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.) or by standard methods known to those skilled in the art.

Degenerate primers are designed to selectively amplify the gene for butyryl-CoA:acetate CoA transferase based on published genomic sequences. Examples of primers are BCoATforward: 5′ GCIGAICATTTCACITGGAAYWSITGGCAYATG (SEQ ID NO: 2047); and BCoATreverse: 5′ CCTGCCTTTGCAATRTCIACRAANGC (SEQ ID NO: 2048), where I=inosine; N=any base; W=A or T; Y=T or C; S=C or G. Amplification is as follows: 1 cycle of 95° C. for 3 min; 40 cycles of 95° C., 53° C., and 72° C. for 30 s each with data acquisition at 72° C.; 1 cycle each of 95° C. and 55° C. for 1 min; and a stepwise increase of the temperature from 55 to 95° C. (at 10 s/0.5° C.) to obtain melting curve data and evaluate product complexity. The target amplicon is about 530 nt in length.

Example 24. Identification of Organisms Harboring Butyrate-Kinase Genes

Butyrate may be produced by substrate level phosphorylation of butyrylCoA by butyrate-kinase and subsequent phosphorylation of ADP to generate ATP and butyrate. DNA isolation and PCR amplification was performed as in Example 23 with the exception that the following primers were used: BUKfor: 5′ GTATAGATTACTIR-YIATHAAYCCNGG (SEQ. ID NO: 2049); and BUKrev: 5′ CAAGCTCRTCIACIACIACNGGRTCNAC (SEQ ID NO: 2050), where I=inosine; N=any base; R=A or G.

Example 25. Identification of Organisms with butyryl-CoA: Acetate CoA Transferase Enzymatic Activity

Bacterial strains are grown overnight in an anaerobic chamber at 37° C. in pre-reduced media selected from those described in Example 9. 10 mL of the bacterial culture is harvested by centrifugation at 10,000 rpm for 10 min, cooled to 4° C. on ice, and disrupted by sonication as described (Duncan, S. et al., 2002 Appl Environ Microbiol Acetate utilization and butyryl coenzyme A (CoA):acetate-CoA transferase in butyrate producing bacteria from the human large intestine 68: 5186-90). ButyrylCoA: acetate CoA transferase activities are determined by the method of Barker, scaled for application to a microtiter plate (Barker H A, et al., 1955 Methods Enzymol 1: 599-600).

Example 26. Identification of Organisms with Butyrate-Kinase, Propionate-Kinase and Acetate-Kinase Enzymatic Activity

Bacterial strains are grown overnight in an anaerobic chamber at 37° C. in pre-reduced media selected from those described in Example 9. 10 mL of the bacterial culture is harvested by centrifugation at 10,000 rpm for 10 min, cooled to 4° C. on ice, and disrupted by sonication as described (Duncan, S. et al., 2002 Appl Environ Microbiol Acetate utilization and butyryl coenzyme A (CoA):acetate-CoA transferase in butyrate producing bacteria from the human large intestine 68: 5186-90). Butyrate-, propionate-, and acetate-kinase activities were determined by colorimetric the method of Rose (Rose I A, 1955 Methods Enzymol Acetate kinase of bacteria 1: 591-5).

Example 27. Characterization of Propionate or Butyrate Production from a Variety of Carbon Sources

Strains identified as having either genes for butyrate or propionate fermentation or having the corresponding enzymatic activities are assayed in vitro using a variety of simple carbon sources for the production of propionate and butyrate. Bacteria are grown overnight in complex media selected from Example 9 in an anaerobic chamber at 37° C. When cultures are visibly turbid, the bacteria are pelleted at 10,000×g for 10 min, the spent media is removed, and they are resuspended in pre-reduced minimal media containing essential vitamins and cofactors (pyridoxamine, p-aminobenzoic acid, biotin, nicotinic acid, folic acid, nicotinamide, choline, pantothenate, riboflavin or vitamin), divalent mineral salts (including the chloride salts of Mg2+, Ca2+ and Mn2+), and organic nitrogenous nutrients (especially glycine, glutamate or asparagine) but lacking carbohydrate as a carbon source. Alternatively, strains may be resuspended in a dilution of the original rich media, for instance a 1:10 or 1:100 dilution, such that essential factors are available but a required carbon source is limiting.

Various carbon sources are added to individual cell suspensions. These include acetate and D and L isomers of lactate, simple sugars including glucose, galactose, mannose, arabinose, xylose or any other naturally sugar, amino sugars such as N-acetyl glucosamine, galactosamine, sialic acid or glucosamine, sugar alcohols such as glycerol, erythritol, threitol, mannitol, inositol or sorbitol. In addition, the cell suspensions are individually incubated with complex carbon sources including di-, tri-, oligo- and polysaccharide carbon sources including fructans, starches, cellulose, galactomannans, xylans, arabinoxylans, pectins, inulin, and fructooligosaccharides. Tested carbon sources also include glycopeptides and glycoproteins, such as mucin. The cell suspension is incubated overnight in a sealed 96-well plate in order prevent the escape of volatile products.

At the end of the incubation period, the production of propionate, butyrate and other SCFAs is determined according to the following protocol:

Reagents

-   -   Internal Standard: 2-ethylbutyric acid, 2-EBA (100 mM)     -   SCFA Mixed Standard: formic acid 10 mM, acetic acid 30 mM,         propionic acid 20 mM, isobutyric acid 5 mM, n-butyric acid 20         mM, n-valeric acid 5 mM, isovaleric acid 5 mM, sodium lactate 10         mM, sodium succinate 10 mM, phenylacetic acid 5 mM     -   MTBSTFA Derivatizing Reagent         (N-Methyl-N-(tert-butyldimethylsilyl)-trifluoroacetamide),         purchased from Regis Technologies     -   Concentrated HCl     -   Deionized Water     -   Diethyl ether (unstabilized)     -   Hexane

Linearity Standards Preparation: Linearity Standard 1 is prepared using straight SCFA Standard. Linearity Standard 2 is prepared using 100 uL of SCFA Standard and 900 uL of water. Linearity Standard 3 is prepared using 100 uL of Linearity Standard 2 and 900 uL of water.

SCFA Extraction:

Extractions of samples (Media and Culture Supernatant), water blanks, and linearity standards were prepared in 4-mL vials using 250 uL of sample, blank, or standard, 250 uL of concentrated HCl, and 50 uL of Internal Standard (2-EBA). Once combined, the sample, standards, and blanks were vortexed and allowed to stand for about 5-10 minutes. Diethyl ether (2000 uL) was added to each of the samples, standards and blanks, and each was liquid-liquid extracted for approximately 2 minutes. The aqueous and organic phases of the extracted samples, standards and blanks were allowed to separate. Once the layers separated, 1000 uL of the ether layer was transferred to 2-mL micro-centrifuge tubes and centrifuged at 14 k for 2 minutes to remove any remaining water.

Sample/Standard/Blank* 250 uL HCl 250 uL Internal Standard (2-EBA) 50 uL Ether 2000 uL *substitute deionized water for blank preparations

Derivatization:

Derivatization of all samples, blanks and standards was conducted in HPLC vials using 175 uL of the upper ether layer of samples or standards and 25 uL of MTBSTFA derivatizing reagent. The reaction mixture was vortexed and allowed to sit at RT for 24 hours. After 24 hours, the ether was removed using a gentle stream of nitrogen, and the residual material was dissolved in 50 uL of hexane. (Note: solvent was removed until no further change in volume was apparent, ˜5-10 min). The derivatized solutions were transferred to small-volume inserts for GC-MS analysis.

An aliquot of the resulting derivatized material is injected into a gas chromatograph (Hewlett Packard 6890) coupled to a mass spectrometer detector (Agilent Technologies 5973). Analyses are completed using DB-5MS (60 m, 0.25 mm i.d., 0.25 mm film coating; P. J. Cobert, St. Louis, Mo.) and electronic impact (70 eV) for ionization. A linear temperature gradient is used. The initial temperature of 80° C. is held for 1 min, then increased to 280° C. (15° C./min) and maintained at 280° C. for 5 min. The source temperature and emission current are 200° C. and 300 mA, respectively. The injector and transfer line temperatures are 250° C. Quantitation is completed in selected ion monitoring acquisition mode by comparison to labeled internal standards [formate was also compared to acetate-13C1,d2]. The m/z ratios of monitored ions for formic acid, acetic acid, propionic acid, butyric acid, acetate, proprionate and butyrate are as follows: 103 (formic acid), 117 (acetic acid), 131 (propionic acid), 145 (butyric acid), 121 ([2H2]- and [1-13C]acetate), 136 ([2H5]propionate), and 149 ([13C4]butyrate).

At the completion of the experiment, a database is generated for each tested organism defining what carbon sources yield which SCFAs. In each case where a microbe is capable of making propionate or butyrate from acetate, lactate, a simple sugar including a disaccharide, an amino sugar or sugar alcohol it is scored as positive for SCFA production. Also noted is whether organisms are capable of utilizing complex carbon sources such as polysaccharides to produce SCFA and which SCFAs are produced.

Example 28. Identification of Organisms Capable of Metabolizing Complex Carbon Sources Including Polysaccharides and Steroids

Individual strains are screened for their ability to metabolize complex carbon sources including polysaccharides and steroids (such as bile salts) according to Example 16 to determine bacterial strain nutrient utilization. For a more complete characterization, specialized plates are constructed utilizing polysaccharide carbon sources including fructans, starches, cellulose, galactomannans, xylans, arabinoxylans, pectins, inulin, and fructooligosaccharides as well as carbon sources including glycopeptides and glycoproteins (such as mucin). These can be made to order by Biolog.

At the end of the experiment, a catalogue of is generated for each tested organism defining what carbon sources it can utilize.

Example 29. Construction of Cross Feeding Compositions

Data from Examples 27 and 28 are analyzed to determine combinations where one organism can make SCFAs from at least one simple carbon source but not from at least one complex carbon source (a polysaccharide or a glycoprotein), and another organism cannot make SCFAs from a simple carbon source but can utilize at least one complex carbon source as a metabolic substrate.

In these cases, a bacterial mixture is made combining a washed overnight culture of the SCFA producer and a washed overnight culture of the SCFA non-producer in a minimal media as described in Example 27 with the addition of the at least one complex carbon source. The bacterial mixture is incubated anaerobically overnight at 37° C. in minimal media or a 1:10 or 1:100 dilution of rich media, and the next day is worked up according to Example 27 in order to detect whether SCFA has been produced. Control cultures include each microbe cultured individually, and the bacterial mixture cultured overnight without the complex carbon source.

Bacterial mixtures in which control cultures do not yield SCFA but the complete mixture does define synergistic bacterial compositions. Synergistic bacterial compositions may be tested for further effects in a variety of in vitro or in vivo models, with and without the complex carbon source, which may be considered a component of one embodiment of the synergistic bacterial composition.

Example 30. In Vivo Validation of Bacterial Composition Efficacy in for Amelioration of Leaky Gut

A murine model for “leaky gut syndrome” is constructed by intraperitoneal injection of pregnant C57BL/6N mice (Charles River, Wilmington, Mass.) with 20 mg/kg poly(I:C) in 200 uL of saline on embryonic day 12.5. Control pregnant mice are injected with 200 uL of saline only (Hsiao E Y et al., 2013 Cell Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders 155: 1451-63).

Pups are randomly selected for treatment with a single bacterial composition or a combination of bacterial compositions at the time of weaning (Day 20-22) and received oral gavage every other day for 6 days. In addition, groups of animals receive mouse chow supplemented with the complex carbohydrate relevant to the bacterial composition(s) that is (are) dosed. Control groups (saline injections) receive comparable combinations of bacterial compositions, with and without the complex carbohydrate.

Animals are tested at adolescence (3 weeks post-weaning) and adulthood (8 weeks post weaning) for leaky gut. Mice are fasted for 4 hr before gavage with 0.6 g/kg 4 kDa FITC-dextran (Sigma Aldrich). Four hours later, serum samples are read for fluorescence intensity at 521 nm using an xFluor4 spectrometer (Tecan). Increased fluorescence is taken as evidence of leaky gut, while decreased fluorescence is evidence for amelioration of leaky gut induced by poly(I:C) treatment. Preferred bacterial compositions decrease leak gut in mice.

Example 31. In Vivo Validation of Bacterial Composition Efficacy in Germ Free Mice Conventionalized with Human Obese Microbiota

Ridaura et al. (2013) showed that germ-free (GF) mice conventionalized with microbiota from female twins discordant for obesity showed taxonomic and phenotypic features of the human donor's microbiota. Mice receiving obese twin microbiota (Ob mice) showed significantly greater body mass and adiposity than recipients of lean twin microbiota (Ln mice). Furthermore, they observed that cohousing Ob mice and Ln mice prevented development of the obese phenotype in the Ob mice and showed that the rescue correlated with invasion of members of the microbiota from the Ln mice into the Ob mice.

Ob and Ln mice prepared as described by Ridaura et al. (2013) can be used to test the therapeutic potential of a bacterial composition for obesity. Ob and Ln mice are generated by introducing via oral gavage fecal samples from twins discordant for obesity into 8-9 week old adult male germ-free C57BL/6J mice. One gnotobiotic isolator is used per microbiota sample and each recipient mouse is individually caged within the isolator. The obese twin must have BMI>30 kg/m2 and the pair must have a sustained multi-year BMI difference of at least 5.5 kg/m2. Recipient mice are fed a low fat (4% by weight) high in plant polysaccharide (LF-HPP), autoclaved mouse chow (B&K Universal, East Yorkshire, U.K. diet 7378000).

To prepare the fecal samples for gavage into the GF mice, fecal samples provided by donors are frozen immediately after production, stored at −80° C. Samples are homogenized by mortar and pestle while submerged in liquid nitrogen and a 500 mg aliquot of the pulverized material is diluted in 5 mL of reduced PBS (PBS supplemented with 0.1% Resazurin (w/v), 0.05% L-cysteine-HCl) in an anaerobic Coy chamber (atmosphere, 75% N2, 20% CO2, 5% H2) and then vortexed for 5 min at room temperature. The suspension is settled by gravity for 5 min, and then the clarified supernatant transferred to an anaerobic crimped tube that is transported to a gnotobiotic mouse facility. Prior to transfer of the tube into the gnotobiotic isolator, the outer surface of the tube is sterilized by exposure for 20 min to chlorine dioxide in the transfer sleeve attached to the isolator. 200 μL aliquot of the suspension is provided into the stomachs of each recipient animal by gavage.

At day 15 post-colonization, the bacterial composition containing at least 108 CFU/ml per strain is administered daily by oral gavage for 4 weeks to half of the Ob mice and half of the Ln mice. The remaining Ob mice and Ln mice are administered PBS by the same regimen. Optionally, mice can receive 0-3 days of antibiotic pre-treatment prior to administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple doses of test article, and 103 to 1010 CFU/ml per strain of a bacterial composition may be delivered. The bacterial composition may optionally be administered together or co-formulated with prebiotic(s).

Feces are collected from the cages for analysis of bacterial carriage. Total body weight, fat mass and lean body mass are measured at baseline before colonization, at days 8 and 15 post-colonization, and days 22, 29, 35, and 42 post-colonization (7, 14, 21, and 28 days after administration of the bacterial composition) using quantitative magnetic resonance analysis of body composition (EchoMRI-3in1 instrument). At time of sacrifice, epididymal fat pads are also collected and weighed. Optionally, luminal contents of the stomach, small intestine, cecum, and colon contents as well as the liver, spleen, and mesenteric lymph nodes can be collected for subsequent analysis. Alternative or additional time points may also be collected.

By the end of the treatment period with the bacterial composition, the Ob mice receiving the bacterial composition is expected to show significant differences in body composition (change in % fat mass; fat pad weight/total body weight) as compared to the Ob group receiving PBS and the Ln groups.

Optionally, at the end of the treatment period, the body composition is determined for all mice. Bacterial compositions that produce significant changes in body composition in the Ob mice (decrease in % fat mass; decrease in fat pad weight; or decrease in total body weight) as compared to control Ob mice receiving PBS are identified as therapeutic candidates.

Example 32. In Vivo Validation of Bacterial Composition Efficacy in Germ Free Mice Conventionalized With Bacterial Composition and Lean/Obese Microbiota Controls

To test the potential of a bacterial composition's ability to treat obesity, 8-9 week old GF C57BL/6J mice can be conventionalized by introducing by oral gavage a) the bacterial composition, b) fecal samples from an obese female twin discordant for obesity (obese control), or c) fecal samples from the paired lean female twin (lean control). One gnotobiotic isolator is used per microbiota sample and each recipient mouse is individually caged within the isolator. The obese twin donors must have BMI>30 kg/m2 and the donating pair must have a sustained multi-year BMI difference of at least 5.5 kg/m2. Recipient mice are fed a low fat (4% by weight) high in plant polysaccharide (LF-HPP), autoclaved mouse chow (B&K Universal, East Yorkshire, U.K. diet 7378000).

To prepare the fecal samples for gavage into the GF mice, fecal samples provided by donors are frozen immediately after production, stored at −80° C. Samples are homogenized by mortar and pestle while submerged in liquid nitrogen and a 500 mg aliquot of the pulverized material is diluted in 5 mL of reduced PBS (PBS supplemented with 0.1% Resazurin (w/v), 0.05% L-cysteine-HCl) in an anaerobic Coy chamber (atmosphere, 75% N2, 20% CO2, 5% H2) and then vortexed for 5 min at room temperature. The suspension is settled by gravity for 5 min, and then the clarified supernatant transferred to an anaerobic crimped tube that is transported to a gnotobiotic mouse facility.

To prepare the bacterial composition for gavage into the GF mice, see Example 9. Prior to transfer of tubes into the gnotobiotic isolator, the outer surface of the tube is sterilized by exposure for 20 min to chlorine dioxide in the transfer sleeve attached to the isolator. 200 μL aliquots of the fecal suspensions are provided into the stomachs of the recipient animals by gavage.

Feces are collected from the cages for analysis of bacterial carriage. Total body weight, fat mass and lean body mass are measured at baseline before colonization, at days 8, 15, 22, 29, and 35. At time of sacrifice, epididymal fat pads are also collected and weighed. Optionally, luminal contents of the stomach, small intestine, cecum, and colon contents as well as the liver, spleen, and mesenteric lymph nodes can be collected for subsequent analysis. Alternative or additional timepoints may also be collected.

By the end of the treatment period with the bacterial composition, the mice receiving the bacterial composition is expected to show body composition (change in % fat mass; fat pad weight/total body weight) and microbial composition that is similar to the lean control and that is statistically different from the obese control.

Example 33. In Vivo Validation of Bacterial Composition Efficacy in Dietary Induced Obesity Mouse Model

Male C57BL/6 mice fed a high fat diet can be used to test bacterial compositions' ability to treat obesity in a diet-induced obesity (DIO mouse) prevention model. To do so, eight groups of mice (n=8) are used, with all combinations of +/− antibiotic pretreatment, bacterial composition vs. vehicle, and high fat vs. standard diet.

4 week old male C57BL/6 mice are group housed (2-5 mice per cage) in filter top cages with autoclaved bedding, and free access to autoclaved irradiated food (LabDiet 5053, LabDiet, St. Louis, Mo. 63144) and autoclaved water. For groups receiving antibiotic pretreatment, drinking water is replaced by an antibiotic cocktail consisting of 10% glucose, kanamycin (0.5 mg/mL), gentamicin (0.044 mg/mL), colistin (1062.5 U/mL), metronidazole (0.269 mg/mL), ciprofloxacin (0.156 mg/mL), ampicillin (0.1 mg/mL) and vancomycin (0.056 mg/mL) (all constituents from Sigma-Aldrich, St. Louis Mo.) for 1 week, after which autoclaved water is returned to all cages. The mice are dosed daily with a volume of 0.2 ml containing at least 1×108 cfu/ml per strain daily or an equal volume of sterile PBS. Optionally, the dose may range from 5×106 to 5×1010 cfu/ml per strain and or dosing may occur three times a week. After one week of dosing, a group (n=10) of mice dosed with vehicle and one with the bacterial composition are switched to a high fat diet (Research Diet D12492) and dosing is continued for all groups. Treatment is continued for 15 weeks following the diet shift. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple doses of test article, and 103 to 1010 CFU/ml per strain of a bacterial composition may be delivered. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Body weight will be measured three times per week throughout the study. Blood will be drawn by submandibular bleed every three weeks, from which serum cholesterol and triglycerides will be measured. Fasting blood glucose will be measured in weeks 12 and 15 following the diet shift. At sacrifice, total body, gastrocnemius, liver, epididymal fat pad, and cecum weights are measured, and the contents of the cecum as well as one lobe of the liver are stored at −80° C. By the end of the experiment, successful treatments will have statistically significant differences in total body weight, epididymal fat pad mass, or cholesterol.

Example 34. In Vivo Validation of Bacterial Composition Efficacy in Nonobese Diabetic Mouse Model of Type-1-Diabetes

To demonstrate the efficacy of the microbial composition for improving the incidence of type 1 diabetes, a type 1 diabetes mouse model described previously is utilized (e.g. see Markle et al 2013. Sex differences in the gut microbiome drive hormone dependent regulation of autoimmunity. Science 339: 1084). Briefly, nonobese diabetic (NOD)/Jsd (NOD) Specific Pathogen Free (SPF) female mice are housed in sterilized static caging. The animals receive a standard mouse diet (LabDiet #5015, PMI Nutrition International) and autoclaved water. All staff uses autoclaved gowns, caps, masks, shoe covers, and sterile gloves. Animal handling and cage changes are done under HEPA filtered air. The pathogen status is determined by weekly exposure of CD-1 sentinel mice to soiled bedding from the cages in the room. Quarterly serological testing of sentinels confirmed the NOD mice are negative for: Mouse Hepatitis Virus, Minute Virus of Mice, Mouse Parvovirus, Murine Norovirus, Sendai Virus, Theiler's Murine Encephalomyelitis, Retrovirus and for endo- and ectoparasites. In addition, live animals are subjected to additional, annual comprehensive testing, including necropsy, histopathology, bacteriology and parasitology testing.

To test the microbial composition for prophylactic ability to reduce, delay or prevent disease appearance, weanling NOD females (aged 22-26 days) are gavaged with 250 uL the microbial bacterial composition using a 24G round tip gavage needle. Recipients are rested for 24 hours, and this procedure is repeated once. Optionally, mice can receive 0-3 days of antibiotic pre-treatment prior to administration with the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple doses of test article, and 103 to 1010 CFU/ml per strain of a bacterial composition may be delivered. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

As a negative control, a group of female weanling NOD mice are gavaged with cecal contents from a female NOD mouse, and as a positive control a third group of female NOD mice are given cecal contents from a male NOD diluted 50× (v/v) and delivered in 250 ul. Spontaneous development of T1D assessment is assessed biweekly by measuring glucose levels in blood and urine. Animals are checked daily and are classified as diabetic when blood glucose exceeds 16 mmol/L or urine glucose exceeds 250 mg/dL. Additionally, serum insulin autoantibody (IAA) is measured by a micro-IAA assay (mIAA). Briefly, 125-I labeled human insulin (Perkin Elmer) is incubated with NOD serum with and without cold (unlabeled) human insulin and the immune complex is isolated by binding to protein A and G Sepharose. The assay is performed on a 96-well filtration plate to retain Sepharose beads and radioactivity is counted on a Topcount 96-well plate beta counter or similar instrument. An index is calculated by taking the difference of cpm between wells without and with cold insulin. A positive is defined by any conventional cut-off measure including a value greater than the 99th percentile of control values, or a value 3 standard deviations beyond the mean of the control values. Furthermore Insulitis is assessed. Briefly, pancreata are dissected and immediately immersed in OCT media (Tissue-Tek, Torrance, Calif.), frozen in −20° C. 2-methylbutane, and stored at −70° C. Preparation of frozen sections is performed with a Leica C M 3050 Cryostat (Leica Canada). To maximize analysis of independent islet infiltrates, three 5-μm sections are cut at least 400 μm apart. Pancreatic sections are stained with Mayer's hematoxylin and eosin Y (H+E, Sigma) to visualize leukocyte infiltration. Assessment of insulitis severity in pancreatic sections is performed by one skilled in the art. Briefly, islets are graded according to the following criteria: 0, no visible infiltrates; 1, peri-insulitis as indicated by peri-vascular and peri-islet infiltrates; 2, <25% of the islet interior 9 occluded by leukocytes displaying invasive infiltrates; 3, >25% but <50% of the islet interior invaded by leukocytes; or 4, invasive insulitis involving 50%-100% of the islet field.

To evaluate the microbial composition for treatment of disease, the procedure above is repeated whereby NOD nonobese diabetic (NOD)/Jsd (NOD) Specific Pathogen Free (SPF) female mice are housed and evaluated for development of diabetes by the criteria described above. Once a mouse develops diabetes it is gavaged with the microbial composition, and blood glucose, urine glucose, and insulin serum levels are evaluated by ELISA weekly to determine disease progression. 7 weeks later animals are sacrificed and insulitis is evaluated by methods described above. Optionally, mice can receive 0-3 days of antibiotic pre-treatment prior to administration with the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple doses of test article, and 103 to 1010 CFU/ml per strain of a bacterial composition may be delivered.

Example 35. In Vivo Validation of Bacterial Composition Efficacy in Nile Rat Model of Type-2-Diabetes

To test the efficacy of a microbial composition for delaying, treating or preventing the symptoms of type 2 diabetes, a Nile grass rat (Arvicanthis niloticus) model described previously is utilized (e.g. see Noda, K., et al. (2010). An animal model of spontaneous metabolic syndrome: Nile grass rat. The FASEB Journal 24, 2443-2453. or Chaabo, F., et al. (2010). Nutritional correlates and dynamics of diabetes in the Nile rat (Arvicanthis niloticus): a novel model for diet-induced type 2 diabetes and the metabolic syndrome. Nutrition & Metabolism 7, 29.). Nile rats, which spontaneously develop symptoms of type 2 diabetes and metabolic syndrome, are individually housed and have free access to autoclaved water and autoclaved standard laboratory chow (Lab Diet 5021; PMI Nutrition, St. Louis, Mo., USA). At 5 weeks of age, thrice-weekly dosing of the Nile rats with about 5×108 cfu/ml per strain of the microbial composition or an equal volume of sterile PBS by oral gavage while under light sedation with 50%/50% O2/CO2 is initiated. Optionally, the dose may range from 5×106 to 5×1010 cfu/ml per strain and/or dosing may occur once weekly. Dosing will continue for 20 weeks post initiation, optionally lasting 15, 30, 40, or 50 weeks. The model could be modified to address prediabetes by shortening the duration to about 3 to 10 weeks post initiation of dosing.

Body weight will be measured three times per week throughout the study. Blood glucose, cholesterol, triglycerides, and hemoglobin A1C will be measured after obtaining blood by tail bleed while under light sedation with 50%/50% O2/CO2 every three weeks following initiation of dosing. At sacrifice, total body, liver, kidney, epididymal fat pad, and cecum weights are measured. Terminal plasma samples are used for measurement of insulin, blood glucose, cholesterol, triglycerides, and hemoglobin A1C. Following perfusion with PBS under deep anesthesia, the liver and kidneys are excised and fixed in 4% paraformaldehyde. Subsequently, 15 μm sections are stained with Oil-Red-O and counterstained with Mayer's hematoxylin to facilitate the identification of stores of hydrophobic lipids. The contents of the cecum are flash frozen in liquid nitrogen and stored at −80° C.

Animals treated with successful compositions will have statistically significant differences in terminal body weight, blood glucose, hemoglobin A1C, liver or kidney accumulation of lipid, and/or insulin from control animals.

Example 36. In Vivo Validation of Bacterial Composition for Prophylactic Use and Treatment in a Mouse Model of Vancomycin Resistant Enterococcus (VRE) Colonization

The emergence and spread of highly antibiotic-resistant bacteria represent a major clinical challenge (Snitkin et al Science Translational Medicine, 2012). In recent years, the numbers of infections caused by organisms such as methicillin-resistant Staphylococcus aureus, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococcus (VRE), and Clostridium difficile have increased markedly, and many of these strains are acquiring resistance to the few remaining active antibiotics. Most infections produced by highly antibiotic-resistant bacteria are acquired during hospitalizations, and preventing patient-to-patient transmission of these pathogens is one of the major challenges confronting hospitals and clinics. Most highly antibiotic-resistant bacterial strains belong to genera that colonize mucosal surfaces, usually at low densities. The highly complex microbiota that normally colonizes mucosal surfaces inhibits expansion of and domination by bacteria such as Enterobacteriaceae and Enterococcaceae. Destruction of the normal flora by antibiotic administration, however, leads to disinhibition antibiotic-resistant members of these bacterial families, enabling to their expansion to very high densities (Ubeda et al Journal of Clinical Investigation 2010). High-density colonization by these organisms can be calamitous for the susceptible patient, resulting in bacteremia and sepsis (Taur et al, Clinical Infectious Disease, 2012).

To test prophylactic use and treatment of a bacterial composition, a VRE infection mouse model is used as previously described (Ubeda et al, Infectious Immunity 2013, Ubeda et al, Journal of Clinical Investigation, 2010). Briefly, experiments are done with 7-week-old C57BL/6J female mice purchased from Jackson Laboratory, housed with irradiated food, and provided with acidified water. Mice are individually housed to avoid exchange of microbiota between mice due to coprophagia. For experimental infections with VRE, mice are treated with ampicillin (0.5 g/liter) in their drinking water, which is changed every 3 days.

In the treatment model, on day 1, mice are infected by means of oral gavage with 108 CFU of the vancomycin-resistant Enterococcus faecium strain purchased from ATCC (ATCC 700221). One day after infection (day 1), antibiotic treatment is stopped and VRE levels are determined at different time points by plating serial dilutions of fecal pellets on Enterococcosel agar plates (Difco) with vancomycin (8 ug/ml; Sigma). VRE colonies are identified by appearance and confirmed by Gram staining or other methods previously described (e.g. see Examples 1,2,3, and 4). In addition, as previously described (Ubeda et al, Journal of Clinical Investigation 2010), PCR of the vanA gene, which confers resistance to vancomycin, confirms the presence of VRE in infected mice. The bacterial composition test article such as but not limited to an ethanol treated, gradient purified spore preparation (as described herein), fecal suspension, or a Network Ecology is delivered in PBS on days 1-3 while the negative control contains only PBS and is also delivered on days 1-3 by oral gavage. Fresh fecal stool pellets are obtained daily for the duration of the experiment from days −7 to day 10. The samples are immediately frozen and stored at −80° C. DNA is extracted using standard techniques and analyzed with 16S or comparable methods (e.g. see Examples 1 and 2).

In the colonization model, ampicillin is administered as described above for day −7 to day 1, treatment with the bacterial composition or vehicle control is administered on day 0-2 and the VRE resistant bacteria at 108 CFU are administered on day 14. Fecal samples are taken throughout the experiment daily from −7 to day 21 and submitted for 16S sequencing as previously described (e.g. see Examples 1 and 2).

In both models, titers of VRE in feces are used to evaluate the success of the bacterial composition versus the negative control. A preferred bacterial composition either prevents or reduces colonization by VRE compared to the negative control, or it accelerates the decrease in colonization after cessation of antibiotics. Furthermore, each bacterial composition is assessed for the ability of the bacterial composition test article to induce a healthy microbiome, as measured by engraftment, augmentation and increase in microbiota diversity.

Example 37. In Vivo Validation of a Bacterial Composition for Prophylactic Use and Treatment of a Mouse Model of Carbapenem Resistant Klebsiella (CRKp) Colonization

The emergence of Klebsiella pneumoniae strains with decreased susceptibility to carbapenems is a significant threat to hospitalized patients. Resistance to carbapenems in these organisms is most frequently mediated by K. pneumoniae carbapenemase (KPC), a class A beta-lactamase that also confers resistance to broad-spectrum cephalosporins and commercially available beta-lactam/beta-lactamase inhibitor combinations (Queenan et al, Clinical Microbiology Review, 2007). KPC-producing K. pneumoniae (KPC-Kp) strains often harbor resistance determinants against several other classes of antimicrobials, including aminoglycosides and fluoroquinolones, resulting in truly multidrug-resistant (MDR) organisms (Hirsch et al, Journal of Antimicrobial Chemotherapy, 2009). Considering the limited antimicrobial options, infections caused by KPC-Kp pose a tremendous therapeutic challenge and are associated with poor clinical outcomes.

A treatment protocol in a mouse model previously described in mice sensitive to KCP-Kp (e.g. Perez et al, Antimicrobial Agents Chemotherapy, 2011) is used to evaluate the bacterial composition (test article) for treating carbapenem resistant Klebsiella and reducing carriage in the GI tract. Female CF1 mice (Harlan Sprague-Dawley, Indianapolis, Ind.) are used and are individually housed and weighed between 25 and 30 g. The bacterial composition includes without limitation an ethanol treated, gradient purified spore preparation (as described herein), fecal suspension, or a Network Ecology.

The thoroughly characterized strain of K. pneumoniae, VA-367 (8, 9, 25) is used. This clinical isolate is genetically related to the KPC-Kp strain circulating in the Eastern United States. Characterization of the resistance mechanisms in K. pneumoniae VA-367 with PCR and DNA sequence analysis revealed the presence of blaKPC-3, blaTEM-1, blaSHV-11, and blaSHV-12 as well as qnrB19 and aac(6′)-lb. Additionally, PCR and DNA sequencing revealed disruptions in the coding sequences of the following outer membrane protein genes: ompK35, ompK36, and ompK37. Antibiotic susceptibility testing (AST) was performed with the agar dilution method and interpreted according to current recommendations from the Clinical and Laboratory Standards Institute (CLSI). A modified Hodge test were performed, according to a method described previously (e.g. see Anderson et al, Journal of Clinical Microbiology, 2007) with ertapenem, meropenem, and imipenem. Tigecycline and polymyxin E were evaluated by Etest susceptibility assays (AB bioMerieux, Solna, Sweden). Results for tigecycline were interpreted as suggested by the U.S. Food and Drug Administration (FDA) and according to CLSI recommendations (criteria for Pseudomonas) for polymyxin E.

In a prophylactic design, mice (10 per group) are assigned to receive either a bacterial composition (test article; e.g. see Example 9 or 10), or control group receiving only the vehicle. After 3 days of subcutaneous clindamycin treatment (Day −6, −5, −4) to sensitize them to KPC-Kp, mice are administered the test article or vehicle daily from day −10 to day 0, On day 0, 103 CFU of KPC-Kp VA-367 diluted in 0.5 ml phosphate-buffered saline (PBS) is administered by oral gavage. Fecal samples are collected 1, 4, 6, and 11 days after the administration of KPC-Kp to measure the concentration of carbapenem-resistant K. pneumoniae. Fecal samples (100 mg diluted in 800 ml of PBS) are plated onto MacConkey agar with 0.5 ug/ml of imipenem, and the number of CFU per gram of stool is determined. Efficacy of test articles is apparent as a reduction in KPC-Kp burden.

Alternatively other methods may be used to measure the levels of carbapenem-resistant K. pneumoniae e.g. PCR, antigen testing, as one who is skilled in the art could perform.

In a treatment design, mice are treated with subcutaneous clindamycin to reduce the normal intestinal flora 1 day before receiving 104 CFU of KPC-Kp VA-367 by oral gavage. For 7 days after oral gavage with KPC-Kp, mice receive oral gavage of normal saline (control group), or the bacterial composition. Fecal samples are collected at baseline and at 3, 6, 8, 11, 16, and 21 days after KPC-Kp VA-367 was given by gavage. The level of CRKp in feces is determined by plating serial dilutions of fecal suspensions to MacConkey agar with 0.5 ug/ml of imipenem, and the number of CFU per gram of stool is determined. Alternatively other methods may be used to measure the levels of carbapenem-resistant K. pneumoniae e.g. PCR, antigen testing, as one who's skilled in the art could perform. Efficacy of test articles is apparent as a reduction in KPC-Kp burden.

Example 38. In Vivo Validation of Bacterial Composition for Efficacy in for the Prophylactic Use or Treatment of Pathogenic Fungus in Mice Models

The bacterial compositions of the invention can be utilized for prophylaxis or treatment of pathogenic fungus in a mouse colonized with one of several Candida species. Adult male CD-1 (ICR) mice are intragastrically inoculated with C. albicans, C. tropicalis or C. parapsilosis as previously described (Mellado et al., Diagnostic Microbiology and Infectious Disease 2000). Tetracycline-HCl at 1 g/L and 5% glucose are included in the drinking water starting on Day −2, 2 days before Candida dosing on Day 0, and throughout the experiment, to enhance colonization. 5×107 Candida are dosed in 0.1 mL on Day 0. By Day 4 all mice are colonized as detected by fecal cfu assay described below. Test articles are used in both prophylactic and treatment regimens. Prophylactic dosing with a bacterial composition including without limitation an ethanol treated, gradient purified spore preparation (as described herein), fecal suspension, or a Network Ecology occurs on Day −1 with a dose between 104 and 1010 bacteria, while treatment dosing occurs on Days 1, 2 and 3 with a similar dose. Negative control groups in both regimes are dosed with PBS administered in a similar manner. All test article dosing is by oral gavage. Treated and untreated mice are kept separate in independently ventilated cages for all of the experiments. Sterilized food, bedding and bottles are used throughout the experiment. Sterilized tap water with or without supplements are also used to avoid contamination. Starting at day −1 postinfection (p.i.), mice are weighed daily and stool samples are collected from each animal and scored for consistency (0, normal feces; 1, mixed stool samples containing both solid and pasty feces; 2, pasty feces; 3, semiliquid feces; 4, liquid feces).

Feces are cultured for yeasts. Dilutions of fecal samples are titrated on Sabouraud Dextrose Chloramphenicol agar (Neogen cat #(7306) agar plates which are selective for fungi. After 24-48 h of incubation at 37° C., quantification of the cultures is achieved by counting the plates visually or by scanning the plates on a Colony Image Analysis Scanner (Spiral Biotech) and processed by the computer software CASBA 4 (Spiral Biotech). The results are noted as colony forming units (CFU) per gram of feces. Effect of bacterial composition on Candida colonization and quality of feces of infected mice is thus analyzed by comparing to placebo, and representative colonies are submitted for 16S/18S/ITS microbial identification before and after infection as previously described (e.g. See Example 1 and 2).

Using this model, the ability of test articles to prevent fungal dissemination and death is also tested. Starting on Day 4 in the above regimen, animals colonized with fungi are treated with immunosuppressive agents to induce deep neutropenia [defined as >500 polymorphonuclear cell per ml. Total white cells counts are performed using a hemacytometer Neubauer improved (Brand, Werthheim/Main, Germany)]. The immunosuppressive agents (150 mg/kg of cyclophosphamide (Sigma) and 65 mg/kg of 6-methyl-prednisolone (Sigma) are both administered intraperitoneally (i.p.) every 72-96 h until deep neutropenia is obtained and continue for 10 days. Test articles are delivered either on Day 4, 5 and 6, in parallel with the start of immunosuppression or for 3 consecutive days after deep neurtopenia is confirmed. Control animals are treated with PBS in each mode of treatment (Day 4-6, or 3 days post neutropenia. Mortality, dissemination and histology are monitored. When animals are severely ill, they are humanely euthanized with pentobarbital (Nembutal) or similar acceptable methods. Dissemination is quantified in kidneys, liver and spleen is quantified by suspending tissue separately in 2 mL of cooled PBS, and homogenizing using a lab-blender (Stomacher 80, Madrid, Spain). Aliquots of the homogenates are cultured for yeasts and bacterial flora. Results are expressed as CFU per gram of tissues. Candida dissemination is defined as positive cultures of at least two cultured organs. Positive culture is defined as plates yielding a value of >1.5 log 10 CFU/g of tissues. Histologic studies are also performed on five cut sections of liver, kidneys and spleen to detect yeasts.

Example 39. In Vivo Validation of Bacterial Composition for Efficacy for Prophylaxis or Treatment in a Mouse Model of Methicillin Resistant Staphylococcus Aureus (MRSA)

Methicillin resistant Staphylococcus aureus (MRSA) is a Gram positive pathogen that is a major cause of nosocomial infections including sepsis, pneumonia and surgical site infections. Both nasal and gastrointestinal carriage of MRSA are implicated as sources of organisms associated with nosocomial infections. Rectal carriage of MRSA is common in patients in intensive care units and patients with both rectal and nasal colonization had significantly higher rates of MRSA infection than did patients with nasal colonization alone (Squier et al Staphylococcus aureus rectal carriage and its association with infections in patients in a surgical intensive care unit and a liver transplant unit. Infect Control Hosp Epidemiol 2002; 23:495-501.)

MRSA is also associated with gastrointestinal disease, including antibiotic associated diarrhea (Boyce and Havill, Nosocomial antibiotic-associated diarrhea associated with enterotoxin-producing strains of methicillin-resistant Staphylococcus aureus. Am J Gastroenterol. 2005 August; 100(8):1828-34; Lo and Bourchardt, Antibiotic-associated diarrhea due to methicillin-resistant Staphylococcus aureus, Diagnostic Microbiology & Infectious Disease 63:388-389, 2009).

A mouse model of MRSA colonization is used to test the efficacy of bacterial compositions in treating MRSA colonization of the gut. CF1 mice are treated with streptomycin (1 mg/ml), delivered in drinking water, for 5 days, after which they are orally inoculated with 1e7 cfu MRSA daily from Day 0 to Day 5 via their drinking water (Gries et al, Growth in Cecal Mucus Facilitates Colonization of the Mouse Intestinal Tract by Methicillin-Resistant Staphylococcus aureus, JID 2005; 192:1621-7). Drinking water is prepared fresh each day. Colonization by MRSA is monitored by determining cfu/ml in feces each day starting on the day prior to the first day of MRSA inoculation. Feces are homogenized in sterile PBS and serial dilutions are plated to Mannitol salt agar and incubated aerobically for 48 h at 37° C. Presumptive MRSA colonies are confirmed by 16S rDNA PCR and sequencing as in (Examples 1 and 2). Bacterial compositions, control PBS or vancomycin are delivered by oral gavage starting on Day 6 for 3 days. Efficacy is observed as a reduction in MRSA cfu/g in feces, and/or faster time to a reduction of MRSA cfu/g, in the animals treated with bacterial compositions but not in control animals. Efficacy is compared to that of the positive control vancomycin, which clears the colonization.

The efficacy of bacterial compositions in preventing MRSA colonization is tested in a mouse model of prophylaxis in which CF1 mice are treated with streptomycin, delivered in drinking water, for 5 days. After 2 days without streptomycin, the mice are treated with bacterial compositions or control PBS by oral gavage for 3 days, and then inoculated with 1e7 cfu MRSA by oral gavage. Colonization by MRSA is monitored by determining cfu/ml in feces each day starting on the day prior to the first day of MRSA inoculation. Feces are homogenized in sterile PBS and serial dilutions are plated to Mannitol salt agar and incubated aerobically for 48 h at 37° C. Presumptive MRSA colonies are confirmed by 16S rDNA PCR and sequencing as in Examples 1 and 2 for 16S sequencing. Efficacy is observed as a reduction in MRSA cfu/g in feces, and/or faster reduction of MRSA cfu/g, in the animals treated with bacterial compositions compared to control animals.

Example 40. Clinical Validation of Bacterial Composition for Efficacy in Obesity

To demonstrate a bacterial composition's ability to treat obesity, a group of 400 obese human subjects can be prospectively recruited. Inclusion criteria include BMI 30-45 kg/m². Exclusion criteria include Type 1 or Type 2 diabetes, treatment with any kind of anti-diabetic, anti-hyperglycemic or anti-obesity medication or surgical procedure (e.g. bariatric surgery), significant co-morbidities, participation in a formal weight loss program, either systolic blood pressure >160 mm Hg or diastolic blood pressure >100 mmHg, subjects whose body weight is not stable, as judged by the Investigator (e.g. >5% change within 3 months prior to screening).

During a double blind treatment period of 12 weeks, the experimental treatment group (n=200) receives a daily oral dose of about 1×109 CFUs of viable bacteria either in the form of vegetative organisms or spores or both, whereas the control group (n=200) is administered a placebo at an identical frequency. The composition can be formulated in a delayed release enteric coated capsule or co-administered with bicarbonate buffer to aid passage of viable organisms through the stomach. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Patients can be optionally treated with a broad spectrum antibiotic 0-10 days prior to first administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple daily doses of test article, and a range of 103 to 1010 CFU of a given composition may be delivered.

At baseline and 6, 12, and 24 weeks after the beginning of the treatment period, change in body weight, waist and hip circumference, and waist/hip ratio will be measured. By the end of the 24 week treatment challenge period, the experimental group is expected to show significant differences from the control group in weight loss and/or waist and hip circumference, optionally 5% or greater weight loss.

Optionally, in the event an effect is detected at the end of the 24 week treatment period, the durability of the effect may be tested. All subjects will be taken off the experimental treatment and change in weight measured after 2 weeks, 4 weeks, 8 weeks, 16 weeks, and 52 weeks.

Example 41. Clinical Validation of Bacterial Composition for Efficacy in Weight Loss

To demonstrate a bacterial composition's ability to cause weight loss, a group of 400 human subjects with BMI>25 kg/m² is prospectively recruited. Inclusion criteria include BMI>25 kg/m². Exclusion criteria include Type 1 or Type 2 diabetes, treatment with any kind of anti-diabetic, anti-hyperglycemic or anti-obesity medication or surgical procedure (e.g. bariatric surgery), significant co-morbidities, participation in a formal weight loss program, either systolic blood pressure >160 mm Hg or diastolic blood pressure >100 mmHg, subjects who do not show stable body weight as judged by PI (e.g. >5% change within 3 months prior to screening).

During a double blind treatment period of 24 weeks, the experimental treatment group (n=200) receives a daily oral dose of about 1×109 CFUs of viable bacteria either in the form of vegetative organisms or spores or both, whereas the control group (n=200) is administered a placebo at an identical frequency. The composition can be formulated in a delayed release enteric coated capsule or co-administered with bicarbonate buffer to aid passage of viable organisms through the stomach. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Patients may be optionally treated with a broad spectrum antibiotic 0-10 days prior to first administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple daily doses of test article, and a range of 103 to 1010 CFU of a given composition may be delivered.

At baseline and 6, 12, and 24 weeks after the beginning of the treatment period, change in body weight will be measured. By the end of the 24 week treatment challenge period, the experimental group are expected to show significant differences from the control group in weight loss.

Optionally, in the event an effect is detected at the end of the 24 week treatment period, the durability of the effect may be tested. All subjects will be taken off the experimental treatment and change in weight measured after 2 weeks, 4 weeks, 8 weeks, 16 weeks, and 52 weeks.

Example 42. Clinical Validation of Bacterial Composition for Efficacy in Prediabetes

To demonstrate a bacterial composition's ability to treat prediabetes by exerting beneficial effects on markers associated with the onset of diabetes, a group of 60 human subjects with metabolic syndrome/prediabetes is prospectively recruited. Inclusion criteria include either (a) fasting plasma glucose between 5.6 and 6.9 mmol/L and 2 hr post-glucose load plasma glucose <7.8 mmol/L, and/or (b) 2 hr post-glucose load plasma glucose in oral glucose tolerance test (OGTT) between 7.8 and 11.0 mmol/L. Exclusion criteria include established gestational, Type 1 or Type 2 diabetes, treatment with any kind of anti-diabetic, anti-hyperglycemic or anti-obesity medication or surgical procedure, use of systemic long-acting corticosteroids or prolonged use (greater than 10 days) of systemic corticosteroids, or any significant medical condition that would complicate the measurement of the endpoint or put the patient at risk.

Optionally, the study can be performed specifically in obese patients meeting the above inclusion criteria with the additional inclusion criteria of BMI 30-45 kg/m² as well as waist circumference >88 cm in women and >102 cm in men. Additional exclusion criteria include: 1) a history of surgical procedures for weight loss; 2) 2 repeat laboratory values at the screening visit of triglycerides >4.52 mmol; and 3) either systolic blood pressure >160 mm Hg or diastolic blood pressure >100 mmHg.

During a double blind treatment period of 12 weeks, the experimental treatment group (n=30) receives a daily oral dose of about 1×109 CFUs of viable bacteria either in the form of vegetative organisms or spores or both, whereas the control group is administered a placebo at an identical frequency (n=30). The composition can be formulated in a delayed release enteric coated capsule or co-administered with bicarbonate buffer to aid passage of viable organisms through the stomach. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Patients can be optionally treated with a broad spectrum antibiotic 0-3 days prior to first administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple daily doses of test article, and a range of 103 to 1011 CFU of a given composition may be delivered.

At baseline and 4, 8 and 12 weeks after the beginning of the treatment period, glucose tolerance is tested by OGTT and HbA1c (glycosylated hemoglobin) levels measured. At the same timepoints, insulin secretion will be assessed by plasma insulin levels measured during the oral glucose tolerance tests. Homeostatic model assessment beta (HOMA-beta) will be used to quantify beta cell function and HOMA-IR for insulin sensitivity. In addition, subjects will perform home blood glucose testing once weekly at home.

By the end of the 12 week treatment period, the experimental group is expected to show significant differences from the control group in glucose tolerance, insulin sensitivity, and/or insulin secretion reflecting improved insulin sensitivity, decreased pre-diabetes symptoms and improvement in metabolic syndrome.

Optionally, in the event an effect is detected at the end of the 12 week treatment period, the durability of the effect may be tested. All subjects will be taken off their respective treatment and return for oral glucose tolerance tests after 2 weeks, 4 weeks, 8 weeks, 16 weeks, and 52 weeks to measure HbA1c, insulin secretion, HOMA-beta, and HOMA-IR.

Optionally, the treatment period can be extended to collect an additional endpoint of progression to type 2 diabetes at 6 months and 12 months after the beginning of the treatment period.

Example 43. Clinical Validation of Bacterial Composition for Efficacy in Type-2-Diabetes

To demonstrate a bacterial composition's ability to treat type 2 diabetes, a group of 60 human subjects with type 2 diabetes is prospectively recruited. Inclusion criteria include diagnosis of type 2 diabetes with inadequate glycemic control on diet and exercise, glycosylated hemoglobin between 7.5% and 10.0% at screening, BMI≤45 kg/m2.

Exclusion criteria include gestational diabetes, type 1 diabetes, treatment with any kind of anti-diabetic medication in the 12 weeks prior to screening, use of anti-obesity medication/surgical procedure, use of systemic long-acting corticosteroids or prolonged use (greater than 10 days) of systemic corticosteroids, or any significant co-morbidities related to the underlying diabetic condition.

Optionally, the study can be done in non insulin dependent type 2 diabetics who have inadequate glycemic control who are taking oral medications such as metformin, sulfonylureas, DPP-4 inhibitors, GLP-1 agonists, and SGLT2 inhibitors. Optionally, the study can be done in newly diagnosed non insulin dependent type 2 diabetics who are completely treatment naive.

During a double-blinded treatment period of 18 weeks, the experimental treatment group (n=30) receives a daily oral dose of about 1×109 CFUs of viable bacteria either in the form of vegetative organisms or spores or both, whereas the control group (n=30) is administered a placebo at an identical frequency. The composition can be formulated in a delayed release enteric coated capsule or co-administered with bicarbonate buffer to aid passage of viable organisms through the stomach. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Patients may be optionally treated with a broad spectrum antibiotic 0-10 days prior to first administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple daily doses of test article, and a range of 103 to 1010 CFUs of a given composition may be delivered.

At baseline and 6, 12 and 18 weeks after the beginning of the treatment period, HbA1c (glycosylated hemoglobin) levels, fasting plasma glucose, fasting insulin, HOMA-beta, and HOMA-IR, In addition, subjects will perform home blood glucose testing once weekly at home.

Optionally high sensitivity C-reactive protein, adiponectin, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, systolic and diastolic blood pressure can also be measured at the same timepoints.

By the end of the 18 week treatment period, the experimental group are expected to show significant differences from the control group in change in HbA1c, fasting plasma glucose, insulin sensitivity, and/or insulin secretion from baseline.

Optionally, in the event an effect is detected at the end of the 18 week treatment period, the durability of the effect may be tested. All subjects will be taken off the experimental treatment and return for measurement of HbA1c, fasting plasma glucose, fasting insulin, HOMA-beta, and HOMA-IR after 2 weeks, 4 weeks, 8 weeks, 16 weeks, and 52 weeks.

Example 44. Clinical Validation of Bacterial Composition for Efficacy in Recent Onset Type-1-Diabetes

To demonstrate a bacterial composition's ability to slow progression of recent onset type 1 diabetes, a group of 60 human subjects with recent onset type 1 diabetes is prospectively assembled.

Inclusion criteria include diagnosis of type 1 diabetes within 40 days prior to screening, positive test for at least one diabetes-related autoantibody such as GAD, IA-2, ZnT8, and/or anti-insulin (obtained within 10 days of onset of insulin therapy), peak stimulated C-peptide level ≥0.2 pmol/mL following mixed meal tolerance test (MMTT), and evidence of some fraction of residual (normal) pancreatic function. Exclusion criteria include any form of diabetes other than type 1 (e.g. type 2 diabetes), prior or current treatment with corticosteroids, significant co-morbidities.

During a double-blind treatment period of 18 weeks, the experimental treatment group (n=30) receives a daily oral dose of about 1×109 CFUs of viable bacteria either in the form of vegetative organisms or spores or both, whereas the control group (n=30) is administered a placebo at an identical frequency. The composition can be formulated in a delayed release enteric coated capsule or co-administered with bicarbonate buffer to aid passage of viable organisms through the stomach. The bacterial composition may be optionally be administered together or co-formulated with prebiotic(s).

Patients can be optionally treated with a broad spectrum antibiotic 0-10 days prior to first administration of the bacterial composition. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple daily doses of test article, and a range of 103 to 1010 CFUs of a given composition are delivered.

At baseline and 6, 12 and 18 weeks after the beginning of the treatment period, stimulated C-peptide released in 2 hours during a standard mixed meal tolerance test (MMTT) and HbA1c levels will be measured. In addition, subjects will record total daily dose of insulin in a diary.

By the end of the 18 week treatment period, the experimental group is expected to show significant differences from the control group in change in stimulated C-peptide, HbA1c, and/or insulin dosage from baseline.

Optionally, in the event an effect is detected at the end of the 18 week treatment period, the durability of the effect may be tested. All subjects will be taken off the experimental treatment and return for measurement of stimulated C-peptide in response to MMTT and HbA1c levels after 2 weeks, 4 weeks, 8 weeks, 16 weeks, and 52 weeks.

Example 45. Clinical Validation of Bacterial Composition for Efficacy in Reduction of Opportunistic Pathogenic Fungus in Humans

The dimorphic yeast, Candida albicans, is the leading fungal pathogen in normal hosts and in patients with damaged immune systems. In immunocompromised hosts such as cancer patients, transplant patients, post-operative surgical patients, premature newborns, or HIV-infected people, C. albicans ranks as the leading fungal pathogen. Invasion leading to systemic infection may also develop in neutropenic patients whose T cell function is comprised. (Hostetter M K, Clinical Microbiology Reviews, January 1994, pp. 29-42.) In this population, disease ranges from aggressive local infections such as periodontitis, oral ulceration, or esophagitis in HIV-infected patients, to complex and potentially lethal infections of the bloodstream with subsequent dissemination to brain, eye, heart, liver, spleen, kidneys, or bone. Recently, the incidence of systemic candidiasis, which is caused by Candida spp., predominantly Candida albicans, has increased. This increase over the last two decades has caused a rise in the use of antifungal drugs, including azoles, such as fluconazole or ketoconazol, leading to emergence of resistant organisms and thus increasing the need for alternative therapies (Looi et al., FEMS Microbiol Lett 2005).

In a prophylactic, randomized, double-blind study, healthy volunteers who have been prescreened as colonized with Candida albicans at >104 cfu/g by fecal culturing are randomized to receive either a placebo or a bacterial composition daily. Study volunteers are asked to avoid taking probiotics in any form in the week prior to dosing. The dosing of bacterial composition may, optionally, be modified to daily, every-other-day, weekly or any other frequency, and doses may range from 105 to 1010 CFU/mL. The subjects provide faecal and vaginal fluid samples pretreatment and on Days 7, 14 and 28 post-treatment that are cultivated on agar plates within 3 hours after delivery to the laboratory. Complementary genomic and microbiological methods are used to characterize the composition of the microbiota from each of the samples. C. albicans is detected by microbiological methods, for example by serial dilution and plating to fungal selective media CHROMagar Candida (BD cat#254093) which selects for fungal organisms, and against bacterial growth, or another fungal selective media, and also by using Taqman PCR based assay using similar methods as described previously (Maaroufi et al., J Clin Microbiol. 2003). A reduction in C. albicans levels in feces indicates efficacy in reducing colonization.

SUMMARY

Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification, including claims, are to be understood as being modified in all instances by the term “about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters are approximations and may vary depending upon the desired properties sought to be obtained. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should be construed in light of the number of significant digits and ordinary rounding approaches.

Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series.

While the invention has been particularly shown and described with reference to a preferred embodiment and various alternate embodiments, it will be understood by persons skilled in the relevant art that various changes in form and details can be made therein without departing from the spirit and scope of the invention.

All references, issued patents and patent applications cited within the body of the instant specification are hereby incorporated by reference in their entirety, for all purposes.

The foregoing description of the embodiments of the invention has been presented for the purpose of illustration; it is not intended to be exhaustive or to limit the invention to the precise forms disclosed. Persons skilled in the relevant art can appreciate that many modifications and variations are possible in light of the above disclosure.

Some portions of this description describe the embodiments of the invention in terms of algorithms and symbolic representations of operations on information. These algorithmic descriptions and representations are commonly used by those skilled in the data processing arts to convey the substance of their work effectively to others skilled in the art. These operations, while described functionally, computationally, or logically, are understood to be implemented by computer programs or equivalent electrical circuits, microcode, or the like. Furthermore, it has also proven convenient at times, to refer to these arrangements of operations as modules, without loss of generality. The described operations and their associated modules may be embodied in software, firmware, hardware, or any combinations thereof.

Any of the steps, operations, or processes described herein may be performed or implemented with one or more hardware or software modules, alone or in combination with other devices. In one embodiment, a software module is implemented with a computer program product comprising a computer-readable medium containing computer program code, which can be executed by a computer processor for performing any or all of the steps, operations, or processes described.

Embodiments of the invention may also relate to an apparatus for performing the operations herein. This apparatus may be specially constructed for the required purposes, and/or it may comprise a general-purpose computing device selectively activated or reconfigured by a computer program stored in the computer. Such a computer program may be stored in a tangible computer readable storage medium or any type of media suitable for storing electronic instructions, and coupled to a computer system bus. Furthermore, any computing systems referred to in the specification may include a single processor or may be architectures employing multiple processor designs for increased computing capability.

Embodiments of the invention may also relate to a computer data signal embodied in a carrier wave, where the computer data signal includes any embodiment of a computer program product or other data combination described herein. The computer data signal is a product that is presented in a tangible medium or carrier wave and modulated or otherwise encoded in the carrier wave, which is tangible, and transmitted according to any suitable transmission method.

Finally, the language used in the specification has been principally selected for readability and instructional purposes, and it may not have been selected to delineate or circumscribe the inventive subject matter. It is therefore intended that the scope of the invention be limited not by this detailed description, but rather by any claims that issue on an application based hereon. Accordingly, the disclosure of the embodiments of the invention is intended to be illustrative, but not limiting, of the scope of the invention, which is set forth in the following claims.

Tables

TABLE 1 SEQ ID Public DB Phylogenetic Spore Pathogen OTU Number Accession Clade Former Status Corynebacterium coyleae 692 X96497 clade_100 N N Corynebacterium mucifaciens 711 NR_026396 clade_100 N N Corynebacterium ureicelerivorans 733 AM397636 clade_100 N N Corynebacterium appendicis 684 NR_028951 clade_102 N N Corynebacterium genitalium 698 ACLJ01000031 clade_102 N N Corynebacterium glaucum 699 NR_028971 clade_102 N N Corynebacterium imitans 703 AF537597 clade_102 N N Corynebacterium riegelii 719 EU848548 clade_102 N N Corynebacterium sp. L_2012475 723 HE575405 clade_102 N N Corynebacterium sp. NML 93_0481 724 GU238409 clade_102 N N Corynebacterium sundsvallense 728 Y09655 clade_102 N N Corynebacterium tuscaniae 730 AY677186 clade_102 N N Prevotella maculosa 1504 AGEK01000035 clade_104 N N Prevotella oris 1513 ADDV01000091 clade_104 N N Prevotella salivae 1517 AB108826 clade_104 N N Prevotella sp. ICM55 1521 HQ616399 clade_104 N N Prevotella sp. oral clone AA020 1528 AY005057 clade_104 N N Prevotella sp. oral clone GI032 1538 AY349396 clade_104 N N Prevotella sp. oral taxon G70 1558 GU432179 clade_104 N N Prevotella corporis 1491 L16465 clade_105 N N Bacteroides sp. 4_1_36 312 ACTC01000133 clade_110 N N Bacteroides sp. AR20 315 AF139524 clade_110 N N Bacteroides sp. D20 319 ACPT01000052 clade_110 N N Bacteroides sp. F_4 322 AB470322 clade_110 N N Bacteroides uniformis 329 AB050110 clade_110 N N Prevotella nanceiensis 1510 JN867228 clade_127 N N Prevotella sp. oral taxon 299 1548 ACWZ01000026 clade_127 N N Prevotella bergensis 1485 ACKS01000100 clade_128 N N Prevotella buccalis 1489 JN867261 clade_129 N N Prevotella timonensis 1564 ADEF01000012 clade_129 N N Prevotella oralis 1512 AEPE01000021 clade_130 N N Prevotella sp. SEQ072 1525 JN867238 clade_130 N N Leuconostoc carnosum 1177 NR_040811 clade_135 N N Leuconostoc gasicomitatum 1179 FN822744 clade_135 N N Leuconostoc inhae 1180 NR_025204 clade_135 N N Leuconostoc kimchii 1181 NR_075014 clade_135 N N Edwardsiella tarda 777 CP002154 clade_139 N N Photorhabdus asymbiotica 1466 Z76752 clade_139 N N Psychrobacter arcticus 1607 CP000082 clade_141 N N Psychrobacter cibarius 1608 HQ698586 clade_141 N N Psychrobacter cryohalolentis 1609 CP000323 clade_141 N N Psychrobacter faecalis 1610 HQ698566 clade_141 N N Psychrobacter nivimaris 1611 HQ698587 clade_141 N N Psychrobacter pulmonis 1612 HQ698582 clade_141 N N Pseudomonas aeruginosa 1592 AABQ07000001 clade_154 N N Pseudomonas sp. 2_1_26 1600 ACWU01000257 clade_154 N N Corynebacterium confusum 691 Y15886 clade_158 N N Corynebacterium propinquum 712 NR_037038 clade_158 N N Corynebacterium pseudodiphtheriticum 713 X84258 clade_158 N N Bartonella bacilliformis 338 NC_008783 clade_159 N N Bartonella grahamii 339 CP001562 clade_159 N N Bartonella henselae 340 NC_005956 clade_159 N N Bartonella quintana 341 BX897700 clade_159 N N Bartonella tamiae 342 EF672728 clade_159 N N Bartonella washoensis 343 FJ719017 clade_159 N N Brucella abortus 430 ACBJ01000075 clade_159 N Category- B Brucella canis 431 NR_044652 clade_159 N Category- B Brucella ceti 432 ACJD01000006 clade_159 N Category- B Brucella melitensis 433 AE009462 clade_159 N Category- B Brucella microti 434 NR_042549 clade_159 N Category- B Brucella ovis 435 NC_009504 clade_159 N Category- B Brucella sp. 83_13 436 ACBQ01000040 clade_159 N Category- B Brucella sp. BO1 437 EU053207 clade_159 N Category- B Brucella suis 438 ACBK01000034 clade_159 N Category- B Ochrobactrum anthropi 1360 NC_009667 clade_159 N N Ochrobactrum intermedium 1361 ACQA01000001 clade_159 N N Ochrobactrum pseudintermedium 1362 DQ365921 clade_159 N N Prevotella genomosp. C2 1496 AY278625 clade_164 N N Prevotella multisaccharivorax 1509 AFJE01000016 clade_164 N N Prevotella sp. oral clone IDR_CEC_0055 1543 AY550997 clade_164 N N Prevotella sp. oral taxon 292 1547 GQ422735 clade_164 N N Prevotella sp. oral taxon 300 1549 GU409549 clade_164 N N Prevotella marshii 1505 AEEI01000070 clade_166 N N Prevotella sp. oral clone IK053 1544 AY349401 clade_166 N N Prevotella sp. oral taxon 781 1554 GQ422744 clade_166 N N Prevotella stercorea 1562 AB244774 clade_166 N N Prevotella brevis 1487 NR_041954 clade_167 N N Prevotella ruminicola 1516 CP002006 clade_167 N N Prevotella sp. sp24 1560 AB003384 clade_167 N N Prevotella sp. sp34 1561 AB003385 clade_167 N N Prevotella albensis 1483 NR_025300 clade_168 N N Prevotella copri 1490 ACBX02000014 clade_168 N N Prevotella oulorum 1514 L16472 clade_168 N N Prevotella sp. BI_42 1518 AJ581354 clade_168 N N Prevotella sp. oral clone P4PB_83 P2 1546 AY207050 clade_168 N N Prevotella sp. oral taxon G60 1557 GU432133 clade_168 N N Prevotella amnii 1484 AB547670 clade_169 N N Bacteroides caccae 268 EU136686 clade_170 N N Bacteroides finegoldii 277 AB222699 clade_170 N N Bacteroides intestinalis 283 ABJL02000006 clade_171 N N Bacteroides sp. XB44A 326 AM230649 clade_171 N N Bifidobacteriaceae genomosp. C1 345 AY278612 clade_172 N N Bifidobacterium adolescentis 346 AAXD02000018 clade_172 N N Bifidobacterium angulatum 347 ABYS02000004 clade_172 N N Bifidobacterium animalis 348 CP001606 clade_172 N N Bifidobacterium breve 350 CP002743 clade_172 N N Bifidobacterium catenulatum 351 ABY01000019 clade_172 N N Bifidobacterium dentium 352 CP001750 clade_172 N OP Bifidobacterium gallicum 353 ABXB03000004 clade_172 N N Bifidobacterium infantis 354 AY151398 clade_172 N N Bifidobacterium kashiwanohense 355 AB491757 clade_172 N N Bifidobacterium longum 356 ABQQ01000041 clade_172 N N Bifidobacterium pseudocatenulatum 357 ABXX02000002 clade_172 N N Bifidobacterium pseudolongum 358 NR_043442 clade_172 N N Bifidobacterium scardovii 359 AJ307005 clade_172 N N Bifidobacterium sp. HM2 360 AB425276 clade_172 N N Bifidobacterium sp. HMLN12 361 JF519685 clade_172 N N Bifidobacterium sp. M45 362 HM626176 clade_172 N N Bifidobacterium sp. MSX5B 363 HQ616382 clade_172 N N Bifidobacterium sp. TM_7 364 AB218972 clade_172 N N Bifidobacterium thermophilum 365 DQ340557 clade_172 N N Leuconostoc citreum 1178 AM157444 clade_175 N N Leuconostoc lactis 1182 NR_040823 clade_175 N N Eubacterium saburreum 858 AB525414 clade_178 Y N Eubacterium sp. oral clone IR009 866 AY349376 clade_178 Y N Lachnospiraceae bacterium ICM62 1061 HQ616401 clade_178 Y N Lachnospiraceae bacterium MSX33 1062 HQ616384 clade_178 Y N Lachnospiraceae bacterium oral taxon 107 1063 ADDS01000069 clade_178 Y N Alicyclobacillus acidocaldarius 122 NR_074721 clade_179 Y N Alicyclobacillus acidoterrestris 123 NR_040844 clade_179 N N Alicyclobacillus cycloheptanicus 125 NR_024754 clade_179 N N Acinetobacter baumannii 27 ACYQ01000014 clade_181 N N Acinetobacter calcoaceticus 28 AM157426 clade_181 N N Acinetobacter genomosp. C1 29 AY278636 clade_181 N N Acinetobacter haemolyticus 30 ADMT01000017 clade_181 N N Acinetobacter johnsonii 31 ACPL01000162 clade_181 N N Acinetobacter junii 32 ACPM01000135 clade_181 N N Acinetobacter lwoffii 33 ACPN01000204 clade_181 N N Acinetobacter parvus 34 AIEB01000124 clade_181 N N Acinetobacter schindleri 36 NR_025412 clade_181 N N Acinetobacter sp. 56A1 37 GQ178049 clade_181 N N Acinetobacter sp. CIP 101934 38 JQ638573 clade_181 N N Acinetobacter sp. CIP 102143 39 JQ638578 clade_181 N N Acinetobacter sp. M16_22 41 HM366447 clade_181 N N Acinetobacter sp. RUH2624 42 ACQF01000094 clade_181 N N Acinetobacter sp. SH024 43 ADCH01000068 clade_181 N N Lactobacillus jensenii 1092 ACQD01000066 clade_182 N N Alcaligenes faecalis 119 AB680368 clade_183 N N Alcaligenes sp. CO14 120 DQ643040 clade_183 N N Alcaligenes sp. S3 121 HQ262549 clade_183 N N Oligella ureolytica 1366 NR_041998 clade_183 N N Oligella urethralis 1367 NR_041753 clade_183 N N Eikenella corrodens 784 ACEA01000028 clade_185 N N Kingella denitrificans 1019 AEWV01000047 clade_185 N N Kingella genomosp. P1 oral cone MB2_C20 1020 DQ003616 clade_185 N N Kingella kingae 1021 AFHS01000073 clade_185 N N Kingella oralis 1022 ACJW02000005 clade_185 N N Kingella sp. oral clone ID059 1023 AY349381 clade_185 N N Neisseria elongata 1330 ADBF01000003 clade_185 N N Neisseria genomosp. P2 oral clone MB5_P15 1332 DQ003630 clade_185 N N Neisseria sp. oral clone JC012 1345 AY349388 clade_185 N N Neisseria sp. SMC_A9199 1342 FJ763637 clade_185 N N Simonsiella muelleri 1731 ADCY01000105 clade_185 N N Corynebacterium glucuronolyticum 700 ABYP01000081 clade_193 N N Corynebacterium pyruviciproducens 716 FJ185225 clade_193 N N Rothia aeria 1649 DQ673320 clade_194 N N Rothia dentocariosa 1650 ADDW01000024 clade_194 N N Rothia sp. oral taxon 188 1653 GU470892 clade_194 N N Corynebacterium accolens 681 ACGD01000048 clade_195 N N Corynebacterium macginleyi 707 AB359393 clade_195 N N Corynebacterium pseudogenitalium 714 ABYQ01000237 clade_195 N N Corynebacterium tuberculostearicum 729 ACVP01000009 clade_195 N N Lactobacillus casei 1074 CP000423 clade_198 N N Lactobacillus paracasei 1106 ABQV01000067 clade_198 N N Lactobacillus zeae 1143 NR_037122 clade_198 N N Prevotella dentalis 1492 AB547678 clade_205 N N Prevotella sp. oral clone ASCG10 1529 AY923148 clade_206 N N Prevotella sp. oral clone HF050 1541 AY349399 clade_206 N N Prevotella sp. oral clone ID019 1542 AY349400 clade_206 N N Prevotella sp. oral clone IK062 1545 AY349402 clade_206 N N Prevotella genomosp. P9 oral clone MB7_G16 1499 DQ003633 clade_207 N N Prevotella sp. oral clone AU069 1531 AY005062 clade_207 N N Prevotella sp. oral clone CY006 1532 AY005063 clade_207 N N Prevotella sp. oral clone FL019 1534 AY349392 clade_207 N N Actinomyces genomosp. C1 56 AY278610 clade_212 N N Actinomyces genomosp. C2 57 AY278611 clade_212 N N Actinomyces genomosp. P1 oral clone MB6_C03 58 DQ003632 clade_212 N N Actinomyces georgiae 59 GU561319 clade_212 N N Actinomyces israelii 60 AF479270 clade_212 N N Actinomyces massiliensis 61 AB545934 clade_212 N N Actinomyces meyeri 62 GU561321 clade_212 N N Actinomyces odontolyticus 66 ACYT01000123 clade_212 N N Actinomyces orihominis 68 AJ571586 clade_212 N N Actinomyces sp. CCUG 37290 71 AJ234058 clade_212 N N Actinomyces sp. ICM34 75 HQ616391 clade_212 N N Actinomyces sp. ICM41 76 HQ616392 clade_212 N N Actinomyces sp. ICM47 77 HQ616395 clade_212 N N Actinomyces sp. ICM54 78 HQ616398 clade_212 N N Actinomyces sp. oral clone IP081 87 AY349366 clade_212 N N Actinomyces sp. oral taxon 178 91 AEUH01000060 clade_212 N N Actinomyces sp. oral taxon 180 92 AEPP01000041 clade_212 N N Actinomyces sp. TeJ5 80 GU561315 clade_212 N N Haematobacter sp. BC14248 968 GU396991 clade_213 N N Paracoccus denitrificans 1424 CP000490 clade_213 N N Paracoccus marcusii 1425 NR_044922 clade_213 N N Grimontia hollisae 967 ADAQ01000013 clade_216 N N Shewanella putrefaciens 1723 CP002457 clade_216 N N Afipia genomosp. 4 111 EU117385 clade_217 N N Rhodopseudomonas palustris 1626 CP000301 clade_217 N N Methylobacterium extorquens 1223 NC_010172 clade_218 N N Methylobacterium podarium 1224 AY468363 clade_218 N N Methylobacterium radiotolerans 1225 GU294320 clade_218 N N Methylobacterium sp. 1sub 1226 AY468371 clade_218 N N Methylobacterium sp. MM4 1227 AY468370 clade_218 N N Clostridium baratii 555 NR_029229 clade_223 Y N Clostridium colicanis 576 FJ957863 clade_223 Y N Clostridium paraputrificum 611 AB536771 clade_223 Y N Clostridium sardiniense 621 NR_041006 clade_223 Y N Eubacterium budayi 837 NR_024682 clade_223 Y N Eubacterium moniliforme 851 HF558373 clade_223 Y N Eubacterium multiforme 852 NR_024683 clade_223 Y N Eubacterium nitritogenes 853 NR_024684 clade_223 Y N Achromobacter denitrificans 18 NR_042021 clade_224 N N Achromobacter piechaudii 19 ADMS01000149 clade_224 N N Achromobacter xylosoxidans 20 ACRC01000072 clade_224 N N Bordetella bronchiseptica 384 NR_025949 clade_224 N OP Bordetella holmesii 385 AB683187 clade_224 N OP Bordetella parapertussis 386 NR_025950 clade_224 N OP Bordetella pertussis 387 BX640418 clade_224 N OP Microbacterium chocolatum 1230 NR_037045 clade_225 N N Microbacterium flavescens 1231 EU714363 clade_225 N N Microbacterium lacticum 1233 EU714351 clade_225 N N Microbacterium oleivorans 1234 EU714381 clade_225 N N Microbacterium oxydans 1235 EU714348 clade_225 N N Microbacterium paraoxydans 1236 AJ491806 clade_225 N N Microbacterium phyllosphaerae 1237 EU714359 clade_225 N N Microbacterium schleiferi 1238 NR_044936 clade_225 N N Microbacterium sp. 768 1239 EU714378 clade_225 N N Microbacterium sp. oral strain C24KA 1240 AF287752 clade_225 N N Microbacterium testaceum 1241 EU714365 clade_225 N N Corynebacterium atypicum 686 NR_025540 clade_229 N N Corynebacterium mastitidis 708 AB359395 clade_229 N N Corynebacterium sp. NML 97_0186 725 GU238411 clade_229 N N Mycobacterium elephantis 1275 AF385898 clade_237 N OP Mycobacterium paraterrae 1288 EU919229 clade_237 N OP Mycobacterium phlei 1289 GU142920 clade_237 N OP Mycobacterium sp. 1776 1293 EU703152 clade_237 N N Mycobacterium sp. 1781 1294 EU703147 clade_237 N N Mycobacterium sp. AQ1GA4 1297 HM210417 clade_237 N N Mycobacterium sp. GN_10546 1299 FJ497243 clade_237 N N Mycobacterium sp. GN_10827 1300 FJ497247 clade_237 N N Mycobacterium sp. GN_11124 1301 FJ652846 clade_237 N N Mycobacterium sp. GN_9188 1302 FJ497240 clade_237 N N Mycobacterium sp. GR_2007_210 1303 FJ555538 clade_237 N N Anoxybacillus contaminans 172 NR_029006 clade_238 N N Anoxybacillus flavithermus 173 NR_074667 clade_238 Y N Bacillus aeolius 195 NR_025557 clade_238 N N Bacillus aerophilus 196 NR_042339 clade_238 Y N Bacillus aestuarii 197 GQ980243 clade_238 Y N Bacillus amyloliquefaciens 199 NR_075005 clade_238 Y N Bacillus anthracis 200 AAEN01000020 clade_238 Y Category- A Bacillus atrophaeus 201 NR_075016 clade_238 Y OP Bacillus badius 202 NR_036893 clade_238 Y OP Bacillus cereus 203 ABDJ01000015 clade_238 Y OP Bacillus circulans 204 AB271747 clade_238 Y OP Bacillus firmus 207 NR_025842 clade_238 Y OP Bacillus flexus 208 NR_024691 clade_238 Y OP Bacillus fordii 209 NR_025786 clade_238 Y OP Bacillus halmapalus 211 NR_026144 clade_238 Y OP Bacillus herbersteinensis 213 NR_042286 clade_238 Y OP Bacillus idriensis 215 NR_043268 clade_238 Y OP Bacillus lentus 216 NR_040792 clade_238 Y OP Bacillus licheniformis 217 NC_006270 clade_238 Y OP Bacillus megaterium 218 GU252124 clade_238 Y OP Bacillus nealsonii 219 NR_044546 clade_238 Y OP Bacillus niabensis 220 NR_043334 clade_238 Y OP Bacillus niacini 221 NR_024695 clade_238 Y OP Bacillus pocheonensis 222 NR_041377 clade_238 Y OP Bacillus pumilus 223 NR_074977 clade_238 Y OP Bacillus safensis 224 JQ624766 clade_238 Y OP Bacillus simplex 225 NR_042136 clade_238 Y OP Bacillus sonorensis 226 NR_025130 clade_238 Y OP Bacillus sp. 10403023 MM10403188 227 CAET01000089 clade_238 Y OP Bacillus sp. 2_A_57_CT2 230 ACWD01000095 clade_238 Y OP Bacillus sp. 2008724126 228 GU252108 clade_238 Y OP Bacillus sp. 2008724139 229 GU252111 clade_238 Y OP Bacillus sp. 7_16AIA 231 FN397518 clade_238 Y OP Bacillus sp. AP8 233 JX101689 clade_238 Y OP Bacillus sp. B27(2008) 234 EU362173 clade_238 Y OP Bacillus sp. BT1B_CT2 235 ACWC01000034 clade_238 Y OP Bacillus sp. GB1.1 236 FJ897765 clade_238 Y OP Bacillus sp. GB9 237 FJ897766 clade_238 Y OP Bacillus sp. HU19.1 238 FJ897769 clade_238 Y OP Bacillus sp. HU29 239 FJ897771 clade_238 Y OP Bacillus sp. HU33.1 240 FJ897772 clade_238 Y OP Bacillus sp. JC6 241 JF824800 clade_238 Y OP Bacillus sp. oral taxon F79 248 HM099654 clade_238 Y OP Bacillus sp. SRC_DSF1 243 GU797283 clade_238 Y OP Bacillus sp. SRC_DSF10 242 GU797292 clade_238 Y OP Bacillus sp. SRC_DSF2 244 GU797284 clade_238 Y OP Bacillus sp. SRC_DSF6 245 GU797288 clade_238 Y OP Bacillus sp. tc09 249 HQ844242 clade_238 Y OP Bacillus sp. zh168 250 FJ851424 clade_238 Y OP Bacillus sphaericus 251 DQ286318 clade_238 Y OP Bacillus sporothermodurans 252 NR_026010 clade_238 Y OP Bacillus subtilis 253 EU627588 clade_238 Y OP Bacillus thermoamylovorans 254 NR_029151 clade_238 Y OP Bacillus thuringiensis 255 NC_008600 clade_238 Y OP Bacillus weihenstephanensis 256 NR_074926 clade_238 Y OP Brevibacterium frigoritolerans 422 NR_042639 clade_238 N N Geobacillus kaustophilus 933 NR_074989 clade_238 Y N Geobacillus sp. E263 934 DQ647387 clade_238 N N Geobacillus sp. WCH70 935 CP001638 clade_238 N N Geobacillus stearothermophilus 936 NR_040794 clade_238 Y N Geobacillus thermocatenulatus 937 NR_043020 clade_238 N N Geobacillus thermodenitrificans 938 NR_074976 clade_238 Y N Geobacillus thermoglucosidasius 939 NR_043022 clade_238 Y N Geobacillus thermoleovorans 940 NR_074931 clade_238 N N Lysinibacillus fusiformis 1192 FN397522 clade_238 N N Lysinibacillus sphaericus 1193 NR_074883 clade_238 Y N Planomicrobium koreense 1468 NR_025011 clade_238 N N Sporosarcina newyorkensis 1754 AFPZ01000142 clade_238 N N Sporosarcina sp. 2681 1755 GU994081 clade_238 N N Ureibacillus composti 1968 NR_043746 clade_238 N N Ureibacillus suwonensis 1969 NR_043232 clade_238 N N Ureibacillus terrenus 1970 NR_025394 clade_238 N N Ureibacillus thermophilus 1971 NR_043747 clade_238 N N Ureibacillus thermosphaericus 1972 NR_040961 clade_238 N N Prevotella micans 1507 AGWK01000061 clade_239 N N Prevotella sp. oral clone DA058 1533 AY005065 clade_239 N N Prevotella sp. SEQ053 1523 JN867222 clade_239 N N Treponema socranskii 1937 NR_024868 clade_240 N OP Treponema sp. 6:H:D15A_4 1938 AY005083 clade_240 N N Treponema sp. oral taxon 265 1953 GU408850 clade_240 N N Treponema sp. oral taxon G85 1958 GU432215 clade_240 N N Porphyromonas endodontalis 1472 ACNN01000021 clade_241 N N Porphyromonas sp. oral clone BB134 1478 AY005068 clade_241 N N Porphyromonas sp. oral clone F016 1479 AY005069 clade_241 N N Porphyromonas sp. oral clone P2PB_52 P1 1480 AY207054 clade_241 N N Porphyromonas sp. oral clone P4GB_100 P2 1481 AY207057 clade_241 N N Acidovorax sp. 98_63833 26 AY258065 clade_245 N N Comamonadaceae bacterium NML000135 663 JN585335 clade_245 N N Comamonadaceae bacterium NML790751 664 JN585331 clade_245 N N Comamonadaceae bacterium NML910035 665 JN585332 clade_245 N N Comamonadaceae bacterium NML910036 666 JN585333 clade_245 N N Comamonas sp. NSP5 668 AB076850 clade_245 N N Delftia acidovorans 748 CP000884 clade_245 N N Xenophilus aerolatus 2018 JN585329 clade_245 N N Clostridiales sp. SS3/4 543 AY305316 clade_246 Y N Oribacterium sp. oral taxon 078 1380 ACIQ02000009 clade_246 N N Oribacterium sp. oral taxon 102 1381 GQ422713 clade_246 N N Weissella cibaria 2007 NR_036924 clade_247 N N Weissella confusa 2008 NR_040816 clade_247 N N Weissella hellenica 2009 AB680902 clade_247 N N Weissella kandleri 2010 NR_044659 clade_247 N N Weissella koreensis 2011 NR_075058 clade_247 N N Weissella paramesenteroides 2012 ACKU01000017 clade_247 N N Weissella sp. KLDS 7.0701 2013 EU600924 clade_247 N N Mobiluncus curtisii 1251 AEPZ01000013 clade_249 N N Clostridium beijerinckii 557 NR_074434 clade_252 Y N Clostridium botulinum 560 NC_010723 clade_252 Y Category- A Clostridium butyricum 561 ABDT01000017 clade_252 Y N Clostridium chauvoei 568 EU106372 clade_252 Y N Clostridium favososporum 582 X76749 clade_252 Y N Clostridium histolyticum 592 HF558362 clade_252 Y N Clostridium isatidis 597 NR_026347 clade_252 Y N Clostridium limosum 602 FR870444 clade_252 Y N Clostridium sartagoforme 622 NR_026490 clade_252 Y N Clostridium septicum 624 NR_026020 clade_252 Y N Clostridium sp. 7_2_43FAA 626 ACDK01000101 clade_252 Y N Clostridium sporogenes 645 ABKW02000003 clade_252 Y N Clostridium tertium 653 Y18174 clade_252 Y N Clostridium carnis 564 NR_044716 clade_253 Y N Clostridium celatum 565 X77844 clade_253 Y N Clostridium disporicum 579 NR_026491 clade_253 Y N Clostridium gasigenes 585 NR_024945 clade_253 Y N Clostridium quinii 616 NR_026149 clade_253 Y N Enhydrobacter aerosaccus 785 ACYI01000081 clade_256 N N Moraxella osloensis 1262 JN175341 clade_256 N N Moraxella sp. GM2 1264 JF837191 clade_256 N N Brevibacterium casei 420 JF951998 clade_257 N N Brevibacterium epidermidis 421 NR_029262 clade_257 N N Brevibacterium sanguinis 426 NR_028016 clade_257 N N Brevibacterium sp. H15 427 AB177640 clade_257 N N Clostridium hylemonae 593 AB023973 clade_260 Y N Clostridium scindens 623 AF262238 clade_260 Y N Lachnospiraceae bacterium 5_1_57FAA 1054 ACTR01000020 clade_260 Y N Acinetobacter radioresistens 35 ACVR01000010 clade_261 N N Clostridium glycyrrhizinilyticum 588 AB233029 clade_262 Y N Clostridium nexile 607 X73443 clade_262 Y N Coprococcus comes 674 ABVR01000038 clade_262 Y N Lachnospiraceae bacterium 1_1_57FAA 1048 ACTM01000065 clade_262 Y N Lachnospiraceae bacterium 1_4_56FAA 1049 ACTN01000028 clade_262 Y N Lachnospiraceae bacterium 8_1_57FAA 1057 ACWQ01000079 clade_262 Y N Ruminococcus lactaris 1663 ABOU02000049 clade_262 Y N Ruminococcus torques 1670 AAVP02000002 clade_262 Y N Lactobacillus alimentarius 1068 NR_044701 clade_263 N N Lactobacillus farciminis 1082 NR_044707 clade_263 N N Lactobacillus kimchii 1097 NR_025045 clade_263 N N Lactobacillus nodensis 1101 NR_041629 clade_263 N N Lactobacillus tucceti 1138 NR_042194 clade_263 N N Pseudomonas mendocina 1595 AAUL01000021 clade_265 N N Pseudomonas pseudoalcaligenes 1598 NR_037000 clade_265 N N Pseudomonas sp. NP522b 1602 EU723211 clade_265 N N Pseudomonas stutzeri 1603 AM905854 clade_265 N N Paenibacillus barcinonensis 1390 NR_042272 clade_270 N N Paenibacillus barengoltzii 1391 NR_042756 clade_270 N N Paenibacillus chibensis 1392 NR_040885 clade_270 N N Paenibacillus cookii 1393 NR_025372 clade_270 N N Paenibacillus durus 1394 NR_037017 clade_270 N N Paenibacillus glucanolyticus 1395 D78470 clade_270 N N Paenibacillus lactis 1396 NR_025739 clade_270 N N Paenibacillus lautus 1397 NR_040882 clade_270 Y N Paenibacillus pabuli 1398 NR_040853 clade_270 N N Paenibacillus polymyxa 1399 NR_037006 clade_270 Y N Paenibacillus popilliae 1400 NR_040888 clade_270 N N Paenibacillus sp. CIP 101062 1401 HM212646 clade_270 N N Paenibacillus sp. HGF5 1402 AEXS01000095 clade_270 Y N Paenibacillus sp. HGF7 1403 AFDH01000147 clade_270 Y N Paenibacillus sp. JC66 1404 JF824808 clade_270 N N Paenibacillus sp. R_27413 1405 HE586333 clade_270 N N Paenibacillus sp. R_27422 1406 HE586338 clade_270 N N Paenibacillus timonensis 1408 NR_042844 clade_270 N N Rothia mucilaginosa 1651 ACVO01000020 clade_271 N N Rothia nasimurium 1652 NR_025310 clade_271 N N Prevotella sp. oral taxon 302 1550 ACZK01000043 clade_280 N N Prevotella sp. oral taxon F68 1556 HM099652 clade_280 N N Prevotella tannerae 1563 ACIJ02000018 clade_280 N N Prevotellaceae bacterium P4P_62 P1 1566 AY207061 clade_280 N N Porphyromonas asaccharolytica 1471 AENO01000048 clade_281 N N Porphyromonas gingivalis 1473 AE015924 clade_281 N N Porphyromonas macacae 1475 NR_025908 clade_281 N N Porphyromonas sp. UQD 301 1477 EU012301 clade_281 N N Porphyromonas uenonis 1482 ACLR01000152 clade_281 N N Leptotrichia buccalis 1165 CP001685 clade_282 N N Leptotrichia hofstadii 1168 ACVB02000032 clade_282 N N Leptotrichia sp. oral clone HE012 1173 AY349386 clade_282 N N Leptotrichia sp. oral taxon 223 1176 GU408547 clade_282 N N Bacteroides fluxus 278 AFBN01000029 clade_285 N N Bacteroides helcogenes 281 CP002352 clade_285 N N Parabacteroides johnsonii 1419 ABYH01000014 clade_286 N N Parabacteroides merdae 1420 EU136685 clade_286 N N Treponema denticola 1926 ADEC01000002 clade_288 N OP Treponema genomosp. P5 oral clone MB3_P23 1929 DQ003624 clade_288 N N Treponema putidum 1935 AJ543428 clade_288 N OP Treponema sp. oral clone P2PB_53 P3 1942 AY207055 clade_288 N N Treponema sp. oral taxon 247 1949 GU408748 clade_288 N N Treponema sp. oral taxon 250 1950 GU408776 clade_288 N N Treponema sp. oral taxon 251 1951 GU408781 clade_288 N N Anaerococcus hydrogenalis 144 ABXA01000039 clade_289 N N Anaerococcus sp. 8404299 148 HM587318 clade_289 N N Anaerococcus sp. gpac215 156 AM176540 clade_289 N N Anaerococcus vaginalis 158 ACXU01000016 clade_289 N N Propionibacterium acidipropionici 1569 NC_019395 clade_290 N N Propionibacterium avidum 1571 AJ003055 clade_290 N N Propionibacterium granulosum 1573 FJ785716 clade_290 N N Propionibacterium jensenii 1574 NR_042269 clade_290 N N Propionibacterium propionicum 1575 NR_025277 clade_290 N N Propionibacterium sp. H456 1577 AB177643 clade_290 N N Propionibacterium thoenii 1581 NR_042270 clade_290 N N Bifidobacterium bifidum 349 ABQP01000027 clade_293 N N Leuconostoc mesenteroides 1183 ACKV01000113 clade_295 N N Leuconostoc pseudomesenteroides 1184 NR_040814 clade_295 N N Eubacterium sp. oral clone JI012 868 AY349379 clade_298 Y N Johnsonella ignava 1016 X87152 clade_298 N N Propionibacterium acnes 1570 ADJM01000010 clade_299 N N Propionibacterium sp. 434_HC2 1576 AFIL01000035 clade_299 N N Propionibacterium sp. LG 1578 AY354921 clade_299 N N Propionibacterium sp. S555a 1579 AB264622 clade_299 N N Alicyclobacillus contaminans 124 NR_041475 clade_301 Y N Alicyclobacillus herbarius 126 NR_024753 clade_301 Y N Alicyclobacillus pomorum 127 NR_024801 clade_301 Y N Alicyclobacillus sp. CCUG 53762 128 HE613268 clade_301 N N Actinomyces cardiffensis 53 GU470888 clade_303 N N Actinomyces funkei 55 HQ906497 clade_303 N N Actinomyces sp. HKU31 74 HQ335393 clade_303 N N Actinomyces sp. oral taxon C55 94 HM099646 clade_303 N N Kerstersia gyiorum 1018 NR_025669 clade_307 N N Pigmentiphaga daeguensis 1467 JN585327 clade_307 N N Aeromonas allosaccharophila 104 S39232 clade_308 N N Aeromonas enteropelogenes 105 X71121 clade_308 N N Aeromonas hydrophila 106 NC_008570 clade_308 N N Aeromonas jandaei 107 X60413 clade_308 N N Aeromonas salmonicida 108 NC_009348 clade_308 N N Aeromonas trota 109 X60415 clade_308 N N Aeromonas veronii 110 NR_044845 clade_308 N N Blautia coccoides 373 AB571656 clade_309 Y N Blautia glucerasea 374 AB588023 clade_309 Y N Blautia glucerasei 375 AB439724 clade_309 Y N Blautia hansenii 376 ABYU02000037 clade_309 Y N Blautia luti 378 AB691576 clade_309 Y N Blautia producta 379 AB600998 clade_309 Y N Blautia schinkii 380 NR_026312 clade_309 Y N Blautia sp. M25 381 HM626178 clade_309 Y N Blautia stercoris 382 HM626177 clade_309 Y N Blautia wexlerae 383 EF036467 clade_309 Y N Bryantella formatexigens 439 ACCL02000018 clade_309 Y N Clostridium coccoides 573 EF025906 clade_309 Y N Eubacterium cellulosolvens 839 AY178842 clade_309 Y N Lachnospiraceae bacterium 6_1_63FAA 1056 ACTV01000014 clade_309 Y N Marvinbryantia formatexigens 1196 AJ505973 clade_309 N N Ruminococcus hansenii 1662 M59114 clade_309 Y N Ruminococcus obeum 1664 AY169419 clade_309 Y N Ruminococcus sp. 5_1_39BFAA 1666 ACII01000172 clade_309 Y N Ruminococcus sp. K_1 1669 AB222208 clade_309 Y N Syntrophococcus sucromutans 1911 NR_036869 clade_309 Y N Rhodobacter sp. oral taxon C30 1620 HM099648 clade_310 N N Rhodobacter sphaeroides 1621 CP000144 clade_310 N N Lactobacillus antri 1071 ACLL01000037 clade_313 N N Lactobacillus coleohominis 1076 ACOH01000030 clade_313 N N Lactobacillus fermentum 1083 CP002033 clade_313 N N Lactobacillus gastricus 1085 AICN01000060 clade_313 N N Lactobacillus mucosae 1099 FR693800 clade_313 N N Lactobacillus oris 1103 AEKL01000077 clade_313 N N Lactobacillus pontis 1111 HM218420 clade_313 N N Lactobacillus reuteri 1112 ACGW02000012 clade_313 N N Lactobacillus sp. KLDS 1.0707 1127 EU600911 clade_313 N N Lactobacillus sp. KLDS 1.0709 1128 EU600913 clade_313 N N Lactobacillus sp. KLDS 1.0711 1129 EU600915 clade_313 N N Lactobacillus sp. KLDS 1.0713 1131 EU600917 clade_313 N N Lactobacillus sp. KLDS 1.0716 1132 EU600921 clade_313 N N Lactobacillus sp. KLDS 1.0718 1133 EU600922 clade_313 N N Lactobacillus sp. oral taxon 052 1137 GQ422710 clade_313 N N Lactobacillus vaginalis 1140 ACGV01000168 clade_313 N N Brevibacterium aurantiacum 419 NR_044854 clade_314 N N Brevibacterium linens 423 AJ315491 clade_314 N N Lactobacillus pentosus 1108 JN813103 clade_315 N N Lactobacillus plantarum 1110 ACGZ02000033 clade_315 N N Lactobacillus sp. KLDS 1.0702 1123 EU600906 clade_315 N N Lactobacillus sp. KLDS 1.0703 1124 EU600907 clade_315 N N Lactobacillus sp. KLDS 1.0704 1125 EU600908 clade_315 N N Lactobacillus sp. KLDS 1.0705 1126 EU600909 clade_315 N N Agrobacterium radiobacter 115 CP000628 clade_316 N N Agrobacterium tumefaciens 116 AJ389893 clade_316 N N Corynebacterium argentoratense 685 EF463055 clade_317 N N Corynebacterium diphtheriae 693 NC_002935 clade_317 N OP Corynebacterium pseudotuberculosis 715 NR_037070 clade_317 N N Corynebacterium renale 717 NR_037069 clade_317 N N Corynebacterium ulcerans 731 NR_074467 clade_317 N N Aurantimonas coralicida 191 AY065627 clade_318 N N Aureimonas altamirensis 192 FN658986 clade_318 N N Lactobacillus acidipiscis 1066 NR_024718 clade_320 N N Lactobacillus salivarius 1117 AEBA01000145 clade_320 N N Lactobacillus sp. KLDS 1.0719 1134 EU600923 clade_320 N N Lactobacillus buchneri 1073 ACGH01000101 clade_321 N N Lactobacillus genomosp. C1 1086 AY278619 clade_321 N N Lactobacillus genomosp. C2 1087 AY278620 clade_321 N N Lactobacillus hilgardii 1089 ACGP01000200 clade_321 N N Lactobacillus kefiri 1096 NR_042230 clade_321 N N Lactobacillus parabuchneri 1105 NR_041294 clade_321 N N Lactobacillus parakefiri 1107 NR_029039 clade_321 N N Lactobacillus curvatus 1079 NR_042437 clade_322 N N Lactobacillus sakei 1116 DQ989236 clade_322 N N Aneurinibacillus aneurinilyticus 167 AB101592 clade_323 N N Aneurinibacillus danicus 168 NR_028657 clade_323 N N Aneurinibacillus migulanus 169 NR_036799 clade_323 N N Aneurinibacillus terranovensis 170 NR_042271 clade_323 N N Staphylococcus aureus 1757 CP002643 clade_325 N Category- B Staphylococcus auricularis 1758 JQ624774 clade_325 N N Staphylococcus capitis 1759 ACFR01000029 clade_325 N N Staphylococcus caprae 1760 ACRH01000033 clade_325 N N Staphylococcus carnosus 1761 NR_075003 clade_325 N N Staphylococcus cohnii 1762 JN175375 clade_325 N N Staphylococcus condimenti 1763 NR_029345 clade_325 N N Staphylococcus epidermidis 1764 ACHE01000056 clade_325 N N Staphylococcus equorum 1765 NR_027520 clade_325 N N Staphylococcus haemolyticus 1767 NC_007168 clade_325 N N Staphylococcus hominis 1768 AM157418 clade_325 N N Staphylococcus lugdunensis 1769 AEQA01000024 clade_325 N N Staphylococcus pasteuri 1770 FJ189773 clade_325 N N Staphylococcus pseudintermedius 1771 CP002439 clade_325 N N Staphylococcus saccharolyticus 1772 NR_029158 clade_325 N N Staphylococcus saprophyticus 1773 NC_007350 clade_325 N N Staphylococcus sp. clone bottae7 1777 AF467424 clade_325 N N Staphylococcus sp. H292 1775 AB177642 clade_325 N N Staphylococcus sp. H780 1776 AB177644 clade_325 N N Staphylococcus succinus 1778 NR_028667 clade_325 N N Staphylococcus warneri 1780 ACPZ01000009 clade_325 N N Staphylococcus xylosus 1781 AY395016 clade_325 N N Cardiobacterium hominis 490 ACKY01000036 clade_326 N N Cardiobacterium valvarum 491 NR_028847 clade_326 N N Pseudomonas fluorescens 1593 AY622220 clade_326 N N Pseudomonas gessardii 1594 FJ943496 clade_326 N N Pseudomonas monteilii 1596 NR_024910 clade_326 N N Pseudomonas poae 1597 GU188951 clade_326 N N Pseudomonas putida 1599 AF094741 clade_326 N N Pseudomonas sp. G1229 1601 DQ910482 clade_326 N N Pseudomonas tolaasii 1604 AF320988 clade_326 N N Pseudomonas viridiflava 1605 NR_042764 clade_326 N N Bacillus alcalophilus 198 X76436 clade_327 Y N Bacillus clausii 205 FN397477 clade_327 Y OP Bacillus gelatini 210 NR_025595 clade_327 Y OP Bacillus halodurans 212 AY144582 clade_327 Y OP Bacillus sp. oral taxon F26 246 HM099642 clade_327 Y OP Listeria grayi 1185 ACCR02000003 clade_328 N OP Listeria innocua 1186 JF967625 clade_328 N N Listeria ivanovii 1187 X56151 clade_328 N N Listeria monocytogenes 1188 CP002003 clade_328 N Category- B Listeria welshimeri 1189 AM263198 clade_328 N OP Capnocytophaga sp. oral clone ASCH05 484 AY923149 clade_333 N N Capnocytophaga sputigena 489 ABZV01000054 clade_333 N N Leptotrichia genomosp. C1 1166 AY278621 clade_334 N N Leptotrichia shahii 1169 AY029806 clade_334 N N Leptotrichia sp. neutropenicPatient 1170 AF189244 clade_334 N N Leptotrichia sp. oral clone GT018 1171 AY349384 clade_334 N N Leptotrichia sp. oral clone GT020 1172 AY349385 clade_334 N N Bacteroides sp. 20_3 296 ACRQ01000064 clade_335 N N Bacteroides sp. 3_1_19 307 ADCJ01000062 clade_335 N N Bacteroides sp. 3_2_5 311 ACIB01000079 clade_335 N N Parabacteroides distasonis 1416 CP000140 clade_335 N N Parabacteroides goldsteinii 1417 AY974070 clade_335 N N Parabacteroides gordonii 1418 AB470344 clade_335 N N Parabacteroides sp. D13 1421 ACPW01000017 clade_335 N N Capnocytophaga genomosp. C1 477 AY278613 clade_336 N N Capnocytophaga ochracea 480 AEOH01000054 clade_336 N N Capnocytophaga sp. GEJ8 481 GU561335 clade_336 N N Capnocytophaga sp. oral strain A47ROY 486 AY005077 clade_336 N N Capnocytophaga sp. S1b 482 U42009 clade_336 N N Paraprevotella clara 1426 AFFY01000068 clade_336 N N Bacteroides heparinolyticus 282 JN867284 clade_338 N N Prevotella heparinolytica 1500 GQ422742 clade_338 N N Treponema genomosp. P4 oral clone MB2_G19 1928 DQ003618 clade_339 N N Treponema genomosp. P6 oral clone MB4_G11 1930 DQ003625 clade_339 N N Treponema sp. oral taxon 254 1952 GU408803 clade_339 N N Treponema sp. oral taxon 508 1956 GU413616 clade_339 N N Treponema sp. oral taxon 518 1957 GU413640 clade_339 N N Chlamydia muridarum 502 AE002160 clade_341 N OP Chlamydia trachomatis 504 U68443 clade_341 N OP Chlamydia psittaci 503 NR_036864 clade_342 N Category- B Chlamydophila pneumoniae 509 NC_002179 clade_342 N OP Chlamydophila psittaci 510 D85712 clade_342 N OP Anaerococcus octavius 146 NR_026360 clade_343 N N Anaerococcus sp. 8405254 149 HM587319 clade_343 N N Anaerococcus sp. 9401487 150 HM587322 clade_343 N N Anaerococcus sp. 9403502 151 HM587325 clade_343 N N Gardnerella vaginalis 923 CP001849 clade_344 N N Campylobacter lari 466 CP000932 clade_346 N OP Anaerobiospirillum succiniciproducens 142 NR_026075 clade_347 N N Anaerobiospirillum thomasii 143 AJ420985 clade_347 N N Ruminobacter amylophilus 1654 NR_026450 clade_347 N N Succinatimonas hippei 1897 AEVO01000027 clade_347 N N Actinomyces europaeus 54 NR_026363 clade_348 N N Actinomyces sp. oral clone GU009 82 AY349361 clade_348 N N Moraxella catarrhalis 1260 CP002005 clade_349 N N Moraxella lincolnii 1261 FR822735 clade_349 N N Moraxella sp. 16285 1263 JF682466 clade_349 N N Psychrobacter sp. 13983 1613 HM212668 clade_349 N N Actinobaculum massiliae 49 AF487679 clade_350 N N Actinobaculum schaalii 50 AY957507 clade_350 N N Actinobaculum sp. BM#101342 51 AY282578 clade_350 N N Actinobaculum sp. P2P_19 P1 52 AY207066 clade_350 N N Actinomyces sp. oral clone IO076 84 AY349363 clade_350 N N Actinomyces sp. oral taxon 848 93 ACUY01000072 clade_350 N N Clostridium innocuum 595 M23732 clade_351 Y N Clostridium sp. HGF2 628 AENW01000022 clade_351 Y N Actinomyces neuii 65 X71862 clade_352 N N Mobiluncus mulieris 1252 ACKW01000035 clade_352 N N Clostridium perfringens 612 ABDW01000023 clade_353 Y Category- B Sarcina ventriculi 1687 NR_026146 clade_353 Y N Clostridium bartlettii 556 ABEZ02000012 clade_354 Y N Clostridium bifermentans 558 X73437 clade_354 Y N Clostridium ghonii 586 AB542933 clade_354 Y N Clostridium glycolicum 587 FJ384385 clade_354 Y N Clostridium mayombei 605 FR733682 clade_354 Y N Clostridium sordellii 625 AB448946 clade_354 Y N Clostridium sp. MT4 E 635 FJ159523 clade_354 Y N Eubacterium tenue 872 M59118 clade_354 Y N Clostridium argentinense 553 NR_029232 clade_355 Y N Clostridium sp. JC122 630 CAEV01000127 clade_355 Y N Clostridium sp. NMBHI_1 636 JN093130 clade_355 Y N Clostridium subterminale 650 NR_041795 clade_355 Y N Clostridium sulfidigenes 651 NR_044161 clade_355 Y N Blastomonas natatoria 372 NR_040824 clade_356 N N Novosphingobium aromaticivorans 1357 AAAV03000008 clade_356 N N Sphingomonas sp. oral clone FI012 1745 AY349411 clade_356 N N Sphingopyxis alaskensis 1749 CP000356 clade_356 N N Oxalobacter formigenes 1389 ACDQ01000020 clade_357 N N Veillonella atypica 1974 AEDS01000059 clade_358 N N Veillonella dispar 1975 ACIK02000021 clade_358 N N Veillonella genomosp. P1 oral clone MB5_P17 1976 DQ003631 clade_358 N N Veillonella parvula 1978 ADFU01000009 clade_358 N N Veillonella sp. 3_1_44 1979 ADCV01000019 clade_358 N N Veillonella sp. 6_1_27 1980 ADCW01000016 clade_358 N N Veillonella sp. ACP1 1981 HQ616359 clade_358 N N Veillonella sp. AS16 1982 HQ616365 clade_358 N N Veillonella sp. BS32b 1983 HQ616368 clade_358 N N Veillonella sp. ICM51a 1984 HQ616396 clade_358 N N Veillonella sp. MSA12 1985 HQ616381 clade_358 N N Veillonella sp. NVG 100cf 1986 EF108443 clade_358 N N Veillonella sp. OK11 1987 JN695650 clade_358 N N Veillonella sp. oral clone ASCG01 1990 AY923144 clade_358 N N Veillonella sp. oral clone ASCG02 1991 AY953257 clade_358 N N Veillonella sp. oral clone OH1A 1992 AY947495 clade_358 N N Veillonella sp. oral taxon 158 1993 AENU01000007 clade_358 N N Dorea formicigenerans 773 AAXA02000006 clade_360 Y N Dorea longicatena 774 AJ132842 clade_360 Y N Lachnospiraceae bacterium 2_1_46FAA 1050 ADLB01000035 clade_360 Y N Lachnospiraceae bacterium 2_1_58FAA 1051 ACTO01000052 clade_360 Y N Lachnospiraceae bacterium 4_1_37FAA 1053 ADCR01000030 clade_360 Y N Lachnospiraceae bacterium 9_1_43BFAA 1058 ACTX01000023 clade_360 Y N Ruminococcus gnavus 1661 X94967 clade_360 Y N Ruminococcus sp. ID8 1668 AY960564 clade_360 Y N Kocuria marina 1040 GQ260086 clade_365 N N Kocuria rhizophila 1042 AY030315 clade_365 N N Kocuria rosea 1043 X87756 clade_365 N N Kocuria varians 1044 AF542074 clade_365 N N Blautia hydrogenotrophica 377 ACBZ01000217 clade_368 Y N Clostridiaceae bacterium END_2 531 EF451053 clade_368 N N Lactonifactor longoviformis 1147 DQ100449 clade_368 Y N Robinsoniella peoriensis 1633 AF445258 clade_368 Y N Micrococcus antarcticus 1242 NR_025285 clade_371 N N Micrococcus luteus 1243 NR_075062 clade_371 N N Micrococcus lylae 1244 NR_026200 clade_371 N N Micrococcus sp. 185 1245 EU714334 clade_371 N N Lactobacillus brevis 1072 EU194349 clade_372 N N Lactobacillus parabrevis 1104 NR_042456 clade_372 N N Pediococcus acidilactici 1436 ACXB01000026 clade_372 N N Pediococcus pentosaceus 1437 NR_075052 clade_372 N N Lactobacillus dextrinicus 1081 NR_036861 clade_373 N N Lactobacillus perolens 1109 NR_029360 clade_373 N N Lactobacillus rhamnosus 1113 ABWJ01000068 clade_373 N N Lactobacillus saniviri 1118 AB602569 clade_373 N N Lactobacillus sp. BT6 1121 HQ616370 clade_373 N N Mycobacterium mageritense 1282 FR798914 clade_374 N OP Mycobacterium neoaurum 1286 AF268445 clade_374 N OP Mycobacterium smegmatis 1291 CP000480 clade_374 N OP Mycobacterium sp. HE5 1304 AJ012738 clade_374 N N Dysgonomonas gadei 775 ADLV01000001 clade_377 N N Dysgonomonas mossii 776 ADLW01000023 clade_377 N N Porphyromonas levii 1474 NR_025907 clade_377 N N Porphyromonas somerae 1476 AB547667 clade_377 N N Bacteroides bamesiae 267 NR_041446 clade_378 N N Bacteroides coprocola 272 ABIY02000050 clade_378 N N Bacteroides coprophilus 273 ACBW01000012 clade_378 N N Bacteroides dorei 274 ABWZ01000093 clade_378 N N Bacteroides massiliensis 284 AB200226 clade_378 N N Bacteroides plebeius 289 AB200218 clade_378 N N Bacteroides sp. 3_1_33FAA 309 ACPS01000085 clade_378 N N Bacteroides sp. 3_1_40A 310 ACRT01000136 clade_378 N N Bacteroides sp. 4_3_47FAA 313 ACDR02000029 clade_378 N N Bacteroides sp. 9_1_42FAA 314 ACAA01000096 clade_378 N N Bacteroides sp. NB_8 323 AB117565 clade_378 N N Bacteroides vulgatus 331 CP000139 clade_378 N N Bacteroides ovatus 287 ACWH01000036 clade_38 N N Bacteroides sp. 1_1_30 294 ADCL01000128 clade_38 N N Bacteroides sp. 2_1_22 297 ACPQ01000117 clade_38 N N Bacteroides sp. 2_2_4 299 ABZZ01000168 clade_38 N N Bacteroides sp. 3_1_23 308 ACRS01000081 clade_38 N N Bacteroides sp. D1 318 ACAB02000030 clade_38 N N Bacteroides sp. D2 321 ACGA01000077 clade_38 N N Bacteroides sp. D22 320 ADCK01000151 clade_38 N N Bacteroides xylanisolvens 332 ADKP01000087 clade_38 N N Treponema lecithinolyticum 1931 NR_026247 clade_380 N OP Treponema parvum 1933 AF302937 clade_380 N OP Treponema sp. oral clone JU025 1940 AY349417 clade_380 N N Treponema sp. oral taxon 270 1954 GQ422733 clade_380 N N Parascardovia denticolens 1428 ADEB01000020 clade_381 N N Scardovia inopinata 1688 AB029087 clade_381 N N Scardovia wiggsiae 1689 AY278626 clade_381 N N Clostridiales bacterium 9400853 533 HM587320 clade_384 N N Eubacterium infirmum 849 U13039 clade_384 Y N Eubacterium sp. WAL 14571 864 FJ687606 clade_384 Y N Mogibacterium diversum 1254 NR_027191 clade_384 N N Mogibacterium neglectum 1255 NR_027203 clade_384 N N Mogibacterium pumilum 1256 NR_028608 clade_384 N N Mogibacterium timidum 1257 Z36296 clade_384 N N Erysipelotrichaceae bacterium 5_2_54FAA 823 ACZW01000054 clade_385 Y N Eubacterium biforme 835 ABYT01000002 clade_385 Y N Eubacterium cylindroides 842 FP929041 clade_385 Y N Eubacterium dolichum 844 L34682 clade_385 Y N Eubacterium sp. 3_1_31 861 ACTL01000045 clade_385 Y N Eubacterium tortuosum 873 NR_044648 clade_385 Y N Borrelia burgdorferi 389 ABGI01000001 clade_386 N OP Borrelia garinii 392 ABJV01000001 clade_386 N OP Borrelia sp. NE49 397 AJ224142 clade_386 N OP Caldimonas manganoxidans 457 NR_040787 clade_387 N N Comamonadaceae bacterium oral taxon F47 667 HM099651 clade_387 N N Lautropia mirabilis 1149 AEQP01000026 clade_387 N N Lautropia sp. oral clone AP009 1150 AY005030 clade_387 N N Bulleidia extructa 441 ADFR01000011 clade_388 Y N Solobacterium moorei 1739 AECQ01000039 clade_388 Y N Peptoniphilus asaccharolyticus 1441 D14145 clade_389 N N Peptoniphilus duerdenii 1442 EU526290 clade_389 N N Peptoniphilus harei 1443 NR_026358 clade_389 N N Peptoniphilus indolicus 1444 AY153431 clade_389 N N Peptoniphilus lacrimalis 1446 ADDO01000050 clade_389 N N Peptoniphilus sp. gpac077 1450 AM176527 clade_389 N N Peptoniphilus sp. JC140 1447 JF824803 clade_389 N N Peptoniphilus sp. oral taxon 386 1452 ADCS01000031 clade_389 N N Peptoniphilus sp. oral taxon 836 1453 AEAA01000090 clade_389 N N Peptostreptococcaceae bacterium ph1 1454 JN837495 clade_389 N N Dialister pneumosintes 765 HM596297 clade_390 N N Dialister sp. oral taxon 502 767 GQ422739 clade_390 N N Cupriavidus metallidurans 741 GU230889 clade_391 N N Herbaspirillum seropedicae 1001 CP002039 clade_391 N N Herbaspirillum sp. JC206 1002 JN657219 clade_391 N N Janthinobacterium sp. SY12 1015 EF455530 clade_391 N N Massilia sp. CCUG 43427A 1197 FR773700 clade_391 N N Ralstonia pickettii 1615 NC_010682 clade_391 N N Ralstonia sp. 5_7_47FAA 1616 ACUF01000076 clade_391 N N Francisella novicida 889 ABSS01000002 clade_392 N N Francisella philomiragia 890 AY928394 clade_392 N N Francisella tularensis 891 ABAZ01000082 clade_392 N Category- A Ignatzschineria indica 1009 HQ823562 clade_392 N N Ignatzschineria sp. NML 95_0260 1010 HQ823559 clade_392 N N Coprococcus catus 673 EU266552 clade_393 Y N Lachnospiraceae bacterium oral taxon F15 1064 HM099641 clade_393 Y N Streptococcus mutans 1814 AP010655 clade_394 N N Clostridium cochlearium 574 NR_044717 clade_395 Y N Clostridium malenominatum 604 FR749893 clade_395 Y N Clostridium tetani 654 NC_004557 clade_395 Y N Acetivibrio ethanolgignens 6 FR749897 clade_396 Y N Anaerosporobacter mobilis 161 NR_042953 clade_396 Y N Bacteroides pectinophilus 288 ABVQ01000036 clade_396 Y N Clostridium aminovalericum 551 NR_029245 clade_396 Y N Clostridium phytofermentans 613 NR_074652 clade_396 Y N Eubacterium hallii 848 L34621 clade_396 Y N Eubacterium xylanophilum 875 L34628 clade_396 Y N Lactobacillus gasseri 1084 ACOZ01000018 clade_398 N N Lactobacillus hominis 1090 FR681902 clade_398 N N Lactobacillus iners 1091 AEKJ01000002 clade_398 N N Lactobacillus johnsonii 1093 AE017198 clade_398 N N Lactobacillus senioris 1119 AB602570 clade_398 N N Lactobacillus sp. oral clone HT002 1135 AY349382 clade_398 N N Weissella beninensis 2006 EU439435 clade_398 N N Sphingomonas echinoides 1744 NR_024700 clade_399 N N Sphingomonas sp. oral taxon A09 1747 HM099639 clade_399 N N Sphingomonas sp. oral taxon F71 1748 HM099645 clade_399 N N Zymomonas mobilis 2032 NR_074274 clade_399 N N Arcanobacterium haemolyticum 174 NR_025347 clade_400 N N Arcanobacterium pyogenes 175 GU585578 clade_400 N N Trueperella pyogenes 1962 NR_044858 clade_400 N N Lactococcus garvieae 1144 AF061005 clade_401 N N Lactococcus lactis 1145 CP002365 clade_401 N N Brevibacterium mcbrellneri 424 ADNU01000076 clade_402 N N Brevibacterium paucivorans 425 EU086796 clade_402 N N Brevibacterium sp. JC43 428 JF824806 clade_402 N N Selenomonas artemidis 1692 HM596274 clade_403 N N Selenomonas sp. FOBRC9 1704 HQ616378 clade_403 N N Selenomonas sp. oral taxon 137 1715 AENV01000007 clade_403 N N Desmospora activa 751 AM940019 clade_404 N N Desmospora sp. 8437 752 AFHT01000143 clade_404 N N Paenibacillus sp. oral taxon F45 1407 HM099647 clade_404 N N Corynebacterium ammoniagenes 682 ADNS01000011 clade_405 N N Corynebacterium aurimucosum 687 ACLH01000041 clade_405 N N Corynebacterium bovis 688 AF537590 clade_405 N N Corynebacterium canis 689 GQ871934 clade_405 N N Corynebacterium casei 690 NR_025101 clade_405 N N Corynebacterium durum 694 Z97069 clade_405 N N Corynebacterium efficiens 695 ACLI01000121 clade_405 N N Corynebacterium falsenii 696 Y13024 clade_405 N N Corynebacterium flavescens 697 NR_037040 clade_405 N N Corynebacterium glutamicum 701 BA000036 clade_405 N N Corynebacterium jeikeium 704 ACYW01000001 clade_405 N OP Corynebacterium kroppenstedtii 705 NR_026380 clade_405 N N Corynebacterium lipophiloflavum 706 ACHJ01000075 clade_405 N N Corynebacterium matruchotii 709 ACSH02000003 clade_405 N N Corynebacterium minutissimum 710 X82064 clade_405 N N Corynebacterium resistens 718 ADGN01000058 clade_405 N N Corynebacterium simulans 720 AF537604 clade_405 N N Corynebacterium singulare 721 NR_026394 clade_405 N N Corynebacterium sp. 1 ex sheep 722 Y13427 clade_405 N N Corynebacterium sp. NML 99_0018 726 GU238413 clade_405 N N Corynebacterium striatum 727 ACGE01000001 clade_405 N OP Corynebacterium urealyticum 732 X81913 clade_405 N OP Corynebacterium variabile 734 NR_025314 clade_405 N N Ruminococcus callidus 1658 NR_029160 clade_406 Y N Ruminococcus champanellensis 1659 FP929052 clade_406 Y N Ruminococcus sp. 18P13 1665 AJ515913 clade_406 Y N Ruminococcus sp. 9SE51 1667 FM954974 clade_406 Y N Aerococcus sanguinicola 98 AY837833 clade_407 N N Aerococcus urinae 99 CP002512 clade_407 N N Aerococcus urinaeequi 100 NR_043443 clade_407 N N Aerococcus viridans 101 ADNT01000041 clade_407 N N Anaerostipes caccae 162 ABAX03000023 clade_408 Y N Anaerostipes sp. 3_2_56FAA 163 ACWB01000002 clade_408 Y N Clostridiales bacterium 1_7_47FAA 541 ABQR01000074 clade_408 Y N Clostridiales sp. SM4_1 542 FP929060 clade_408 Y N Clostridiales sp. SSC_2 544 FP929061 clade_408 Y N Clostridium aerotolerans 546 X76163 clade_408 Y N Clostridium aldenense 547 NR_043680 clade_408 Y N Clostridium algidixylanolyticum 550 NR_028726 clade_408 Y N Clostridium amygdalinum 552 AY353957 clade_408 Y N Clostridium asparagiforme 554 ACCJ01000522 clade_408 Y N Clostridium bolteae 559 ABCC02000039 clade_408 Y N Clostridium celerecrescens 566 JQ246092 clade_408 Y N Clostridium citroniae 569 ADLJ01000059 clade_408 Y N Clostridium clostridiiformes 571 M59089 clade_408 Y N Clostridium clostridioforme 572 NR_044715 clade_408 Y N Clostridium hathewayi 590 AY552788 clade_408 Y N Clostridium indolis 594 AF028351 clade_408 Y N Clostridium lavalense 600 EF564277 clade_408 Y N Clostridium saccharolyticum 620 CP002109 clade_408 Y N Clostridium sp. M62_1 633 ACFX02000046 clade_408 Y N Clostridium sp. SS2_1 638 ABGC03000041 clade_408 Y N Clostridium sphenoides 643 X73449 clade_408 Y N Clostridium symbiosum 652 ADLQ01000114 clade_408 Y N Clostridium xylanolyticum 658 NR_037068 clade_408 Y N Eubacterium hadrum 847 FR749933 clade_408 Y N Fusobacterium naviforme 898 HQ223106 clade_408 N N Lachnospiraceae bacterium 3_1_57FAA 1052 ACTP01000124 clade_408 Y N Lachnospiraceae bacterium 5_1_63FAA 1055 ACTS01000081 clade_408 Y N Lachnospiraceae bacterium A4 1059 DQ789118 clade_408 Y N Lachnospiraceae bacterium DJF VP30 1060 EU728771 clade_408 Y N Lachnospiraceae genomosp. C1 1065 AY278618 clade_408 Y N Moryella indoligenes 1268 AF527773 clade_408 N N Clostridium difficile 578 NC_013315 clade_409 Y OP Selenomonas genomosp. P5 1697 AY341820 clade_410 N N Selenomonas sp. oral clone IQ048 1710 AY349408 clade_410 N N Selenomonas sputigena 1717 ACKP02000033 clade_410 N N Hyphomicrobium sulfonivorans 1007 AY468372 clade_411 N N Methylocella silvestris 1228 NR_074237 clade_411 N N Legionella pneumophila 1153 NC_002942 clade_412 N OP Lactobacillus coryniformis 1077 NR_044705 clade_413 N N Arthrobacter agilis 178 NR_026198 clade_414 N N Arthrobacter arilaitensis 179 NR_074608 clade_414 N N Arthrobacter bergerei 180 NR_025612 clade_414 N N Arthrobacter globiformis 181 NR_026187 clade_414 N N Arthrobacter nicotianae 182 NR_026190 clade_414 N N Mycobacterium abscessus 1269 AGQU01000002 clade_418 N OP Mycobacterium chelonae 1273 AB548610 clade_418 N OP Bacteroides salanitronis 291 CP002530 clade_419 N N Paraprevotella xylaniphila 1427 AFBR01000011 clade_419 N N Barnesiella intestinihominis 336 AB370251 clade_420 N N Barnesiella viscericola 337 NR_041508 clade_420 N N Parabacteroides sp. NS31_3 1422 JN029805 clade_420 N N Porphyromonadaceae bacterium NML 060648 1470 EF184292 clade_420 N N Tannerella forsythia 1913 CP003191 clade_420 N N Tannerella sp. 6_1_58FAA_CT1 1914 ACWX01000068 clade_420 N N Mycoplasma amphoriforme 1311 AY531656 clade_421 N N Mycoplasma genitalium 1317 L43967 clade_421 N N Mycoplasma pneumoniae 1322 NC_000912 clade_421 N N Mycoplasma penetrans 1321 NC_004432 clade_422 N N Ureaplasma parvum 1966 AE002127 clade_422 N N Ureaplasma urealyticum 1967 AAYN01000002 clade_422 N N Treponema genomosp. P1 1927 AY341822 clade_425 N N Treponema sp. oral taxon 228 1943 GU408580 clade_425 N N Treponema sp. oral taxon 230 1944 GU408603 clade_425 N N Treponema sp. oral taxon 231 1945 GU408631 clade_425 N N Treponema sp. oral taxon 232 1946 GU408646 clade_425 N N Treponema sp. oral taxon 235 1947 GU408673 clade_425 N N Treponema sp. ovine footrot 1959 AJ010951 clade_425 N N Treponema vincentii 1960 ACYH01000036 clade_425 N OP Eubacterium sp. AS15b 862 HQ616364 clade_428 Y N Eubacterium sp. OBRC9 863 HQ616354 clade_428 Y N Eubacterium sp. oral clone OH3A 871 AY947497 clade_428 Y N Eubacterium yurii 876 AEES01000073 clade_428 Y N Clostridium acetobutylicum 545 NR_074511 clade_430 Y N Clostridium algidicarnis 549 NR_041746 clade_430 Y N Clostridium cadaveris 562 AB542932 clade_430 Y N Clostridium carboxidivorans 563 FR733710 clade_430 Y N Clostridium estertheticum 580 NR_042153 clade_430 Y N Clostridium fallax 581 NR_044714 clade_430 Y N Clostridium felsineum 583 AF270502 clade_430 Y N Clostridium frigidicarnis 584 NR_024919 clade_430 Y N Clostridium kluyveri 598 NR_074165 clade_430 Y N Clostridium magnum 603 X77835 clade_430 Y N Clostridium putrefaciens 615 NR_024995 clade_430 Y N Clostridium sp. HPB_46 629 AY862516 clade_430 Y N Clostridium tyrobutyricum 656 NR_044718 clade_430 Y N Burkholderiales bacterium 1_1_47 452 ADCQ01000066 clade_432 N OP Parasutterella excrementihominis 1429 AFBP01000029 clade_432 N N Parasutterella secunda 1430 AB491209 clade_432 N N Sutterella morbirenis 1898 AJ832129 clade_432 N N Sutterella parvirubra 1899 AB300989 clade_432 Y N Sutterella sanguinus 1900 AJ748647 clade_432 N N Sutterella sp. YIT 12072 1901 AB491210 clade_432 N N Sutterella stercoricanis 1902 NR_025600 clade_432 N N Sutterella wadsworthensis 1903 ADMF01000048 clade_432 N N Propionibacterium freudenreichii 1572 NR_036972 clade_433 N N Propionibacterium sp. oral taxon 192 1580 GQ422728 clade_433 N N Tessaracoccus sp. oral taxon F04 1917 HM099640 clade_433 N N Peptoniphilus ivorii 1445 Y07840 clade_434 N N Peptoniphilus sp. gpac007 1448 AM176517 clade_434 N N Peptoniphilus sp. gpac018A 1449 AM176519 clade_434 N N Peptoniphilus sp. gpac148 1451 AM176535 clade_434 N N Flexispira rappini 887 AY126479 clade_436 N N Helicobacter bilis 993 ACDN01000023 clade_436 N N Helicobacter cinaedi 995 ABQT01000054 clade_436 N N Helicobacter sp. None 998 U44756 clade_436 N N Brevundimonas subvibrioides 429 CP002102 clade_438 N N Hyphomonas neptunium 1008 NR_074092 clade_438 N N Phenylobacterium zucineum 1465 AY628697 clade_438 N N Acetanaerobacterium elongatum 4 NR_042930 clade_439 Y N Clostridium cellulosi 567 NR_044624 clade_439 Y N Ethanoligenens harbinense 832 AY675965 clade_439 Y N Streptococcus downei 1793 AEKN01000002 clade_441 N N Streptococcus sp. SHV515 1848 Y07601 clade_441 N N Acinetobacter sp. CIP 53.82 40 JQ638584 clade_443 N N Halomonas elongata 990 NR_074782 clade_443 N N Halomonas johnsoniae 991 FR775979 clade_443 N N Butyrivibrio fibrisolvens 456 U41172 clade_444 N N Eubacterium rectale 856 FP929042 clade_444 Y N Eubacterium sp. oral clone GI038 865 AY349374 clade_444 Y N Lachnobacterium bovis 1045 GU324407 clade_444 Y N Roseburia cecicola 1634 GU233441 clade_444 Y N Roseburia faecalis 1635 AY804149 clade_444 Y N Roseburia faecis 1636 AY305310 clade_444 Y N Roseburia hominis 1637 AJ270482 clade_444 Y N Roseburia intestinalis 1638 FP929050 clade_444 Y N Roseburia inulinivorans 1639 AJ270473 clade_444 Y N Roseburia sp. 11SE37 1640 FM954975 clade_444 N N Roseburia sp. 11SE38 1641 FM954976 clade_444 N N Shuttleworthia satelles 1728 ACIP02000004 clade_444 N N Shuttleworthia sp. MSX8B 1729 HQ616383 clade_444 N N Shuttleworthia sp. oral taxon G69 1730 GU432167 clade_444 N N Bdellovibrio sp. MPA 344 AY294215 clade_445 N N Desulfobulbus sp. oral clone CH031 755 AY005036 clade_445 N N Desulfovibrio desulfuricans 757 DQ092636 clade_445 N N Desulfovibrio fairfieldensis 758 U42221 clade_445 N N Desulfovibrio piger 759 AF192152 clade_445 N N Desulfovibrio sp. 3_l_syn3 760 ADDR01000239 clade_445 N N Geobacter bemidjiensis 941 CP001124 clade_445 N N Brachybacterium alimentarium 401 NR_026269 clade_446 N N Brachybacterium conglomeratum 402 AB537169 clade_446 N N Brachybacterium tyrofermentans 403 NR_026272 clade_446 N N Dermabacter hominis 749 FJ263375 clade_446 N N Aneurinibacillus thermoaerophilus 171 NR_029303 clade_448 N N Brevibacillus agri 409 NR_040983 clade_448 N N Brevibacillus brevis 410 NR_041524 clade_448 Y N Brevibacillus centrosporus 411 NR_043414 clade_448 N N Brevibacillus choshinensis 412 NR_040980 clade_448 N N Brevibacillus invocatus 413 NR_041836 clade_448 N N Brevibacillus laterosporus 414 NR_037005 clade_448 Y N Brevibacillus parabrevis 415 NR_040981 clade_448 N N Brevibacillus reuszeri 416 NR_040982 clade_448 N N Brevibacillus sp. phR 417 JN837488 clade_448 N N Brevibacillus thermoruber 418 NR_026514 clade_448 N N Lactobacillus murinus 1100 NR_042231 clade_449 N N Lactobacillus oeni 1102 NR_043095 clade_449 N N Lactobacillus ruminis 1115 ACGS02000043 clade_449 N N Lactobacillus vini 1141 NR_042196 clade_449 N N Gemella haemolysans 924 ACDZ02000012 clade_450 N N Gemella morbillorum 925 NR_025904 clade_450 N N Gemella morbillorum 926 ACRX01000010 clade_450 N N Gemella sanguinis 927 ACRY01000057 clade_450 N N Gemella sp. oral clone ASCE02 929 AY923133 clade_450 N N Gemella sp. oral clone ASCF04 930 AY923139 clade_450 N N Gemella sp. oral clone ASCF12 931 AY923143 clade_450 N N Gemella sp. WAL 1945J 928 EU427463 clade_450 N N Bacillus coagulans 206 DQ297928 clade_451 Y OP Sporolactobacillus inulinus 1752 NR_040962 clade_451 Y N Sporolactobacillus nakayamae 1753 NR_042247 clade_451 N N Gluconacetobacter entanii 945 NR_028909 clade_452 N N Gluconacetobacter europaeus 946 NR_026513 clade_452 N N Gluconacetobacter hansenii 947 NR_026133 clade_452 N N Gluconacetobacter oboediens 949 NR_041295 clade_452 N N Gluconacetobacter xylinus 950 NR_074338 clade_452 N N Auritibacter ignavus 193 FN554542 clade_453 N N Dermacoccus sp. Ellin185 750 AEIQ01000090 clade_453 N N Janibacter limosus 1013 NR_026362 clade_453 N N Janibacter melonis 1014 EF063716 clade_453 N N Kocuria palustris 1041 EU333884 clade_453 Y N Acetobacter aceti 7 NR_026121 clade_454 N N Acetobacter fabarum 8 NR_042678 clade_454 N N Acetobacter lovaniensis 9 NR_040832 clade_454 N N Acetobacter malorum 10 NR_025513 clade_454 N N Acetobacter orientalis 11 NR_028625 clade_454 N N Acetobacter pasteurianus 12 NR_026107 clade_454 N N Acetobacter pomorum 13 NR_042112 clade_454 N N Acetobacter syzygii 14 NR_040868 clade_454 N N Acetobacter tropicalis 15 NR_036881 clade_454 N N Gluconacetobacter azotocaptans 943 NR_028767 clade_454 N N Gluconacetobacter diazotrophicus 944 NR_074292 clade_454 N N Gluconacetobacter johannae 948 NR_024959 clade_454 N N Nocardia brasiliensis 1351 AIHV01000038 clade_455 N N Nocardia cyriacigeorgica 1352 HQ009486 clade_455 N N Nocardia farcinica 1353 NC_006361 clade_455 Y N Nocardia puris 1354 NR_028994 clade_455 N N Nocardia sp. 01_Je_025 1355 GU574059 clade_455 N N Rhodococcus equi 1623 ADNW01000058 clade_455 N N Bacillus sp. oral taxon F28 247 HM099650 clade_456 Y OP Oceanobacillus caeni 1358 NR_041533 clade_456 N N Oceanobacillus sp. Ndiop 1359 CAER01000083 clade_456 N N Ornithinibacillus bavariensis 1384 NR_044923 clade_456 N N Ornithinibacillus sp. 7_10AIA 1385 FN397526 clade_456 N N Virgibacillus proomii 2005 NR_025308 clade_456 N N Corynebacterium amycolatum 683 ABZU01000033 clade_457 N OP Corynebacterium hansenii 702 AM946639 clade_457 N N Corynebacterium xerosis 735 FN179330 clade_457 N OP Staphylococcaceae bacterium NML 92_0017 1756 AY841362 clade_458 N N Staphylococcus fleurettii 1766 NR_041326 clade_458 N N Staphylococcus sciuri 1774 NR_025520 clade_458 N N Staphylococcus vitulinus 1779 NR_024670 clade_458 N N Stenotrophomonas maltophilia 1782 AAVZ01000005 clade_459 N N Stenotrophomonas sp. FG_6 1783 EF017810 clade_459 N N Mycobacterium africanum 1270 AF480605 clade_46 N OP Mycobacterium alsiensis 1271 AJ938169 clade_46 N OP Mycobacterium avium 1272 CP000479 clade_46 N OP Mycobacterium colombiense 1274 AM062764 clade_46 N OP Mycobacterium gordonae 1276 GU142930 clade_46 N OP Mycobacterium intracellulare 1277 GQ153276 clade_46 N OP Mycobacterium kansasii 1278 AF480601 clade_46 N OP Mycobacterium lacus 1279 NR_025175 clade_46 N OP Mycobacterium leprae 1280 FM211192 clade_46 N OP Mycobacterium lepromatosis 1281 EU203590 clade_46 N OP Mycobacterium mantenii 1283 FJ042897 clade_46 N OP Mycobacterium marinum 1284 NC_010612 clade_46 N OP Mycobacterium microti 1285 NR_025234 clade_46 N OP Mycobacterium parascrofulaceum 1287 ADNV01000350 clade_46 N OP Mycobacterium seoulense 1290 DQ536403 clade_46 N OP Mycobacterium sp. 1761 1292 EU703150 clade_46 N N Mycobacterium sp. 1791 1295 EU703148 clade_46 N N Mycobacterium sp. 1797 1296 EU703149 clade_46 N N Mycobacterium sp. B10_07.09.0206 1298 HQ174245 clade_46 N N Mycobacterium sp. NLA001000736 1305 HM627011 clade_46 N N Mycobacterium sp. W 1306 DQ437715 clade_46 N N Mycobacterium tuberculosis 1307 CP001658 clade_46 N Category- C Mycobacterium ulcerans 1308 AB548725 clade_46 N OP Mycobacterium vulneris 1309 EU834055 clade_46 N OP Xanthomonas campestris 2016 EF101975 clade_461 N N Xanthomonas sp. kmd_489 2017 EU723184 clade_461 N N Dietzia natronolimnaea 769 GQ870426 clade_462 N N Dietzia sp. BBDP51 770 DQ337512 clade_462 N N Dietzia sp. CA149 771 GQ870422 clade_462 N N Dietzia timorensis 772 GQ870424 clade_462 N N Gordonia bronchialis 951 NR_027594 clade_463 N N Gordonia polyisoprenivorans 952 DQ385609 clade_463 N N Gordonia sp. KTR9 953 DQ068383 clade_463 N N Gordonia sputi 954 FJ536304 clade_463 N N Gordonia terrae 955 GQ848239 clade_463 N N Leptotrichia goodfellowii 1167 ADAD01000110 clade_465 N N Leptotrichia sp. oral clone IK040 1174 AY349387 clade_465 N N Leptotrichia sp. oral clone P2PB_51 P1 1175 AY207053 clade_465 N N Bacteroidales genomosp. P7 oral clone MB3_P19 264 DQ003623 clade_466 N N Butyricimonas virosa 454 AB443949 clade_466 N N Odoribacter laneus 1363 AB490805 clade_466 N N Odoribacter splanchnicus 1364 CP002544 clade_466 N N Capnocytophaga gingivalis 478 ACLQ01000011 clade_467 N N Capnocytophaga granulosa 479 X97248 clade_467 N N Capnocytophaga sp. oral clone AH015 483 AY005074 clade_467 N N Capnocytophaga sp. oral strain S3 487 AY005073 clade_467 N N Capnocytophaga sp. oral taxon 338 488 AEXX01000050 clade_467 N N Capnocytophaga canimorsus 476 CP002113 clade_468 N N Capnocytophaga sp. oral clone ID062 485 AY349368 clade_468 N N Catenibacterium mitsuokai 495 AB030224 clade_469 Y N Clostridium sp. TM_40 640 AB249652 clade_469 Y N Coprobacillus cateniformis 670 AB030218 clade_469 Y N Coprobacillus sp. 29_1 671 ADKX01000057 clade_469 Y N Lactobacillus catenaformis 1075 M23729 clade_469 N N Lactobacillus vitulinus 1142 NR_041305 clade_469 N N Cetobacterium somerae 501 AJ438155 clade_470 N N Clostridium rectum 618 NR_029271 clade_470 Y N Fusobacterium gonidiaformans 896 ACET01000043 clade_470 N N Fusobacterium mortiferum 897 ACDB02000034 clade_470 N N Fusobacterium necrogenes 899 X55408 clade_470 N N Fusobacterium necrophorum 900 AM905356 clade_470 N N Fusobacterium sp. 12_1B 905 AGWJ01000070 clade_470 N N Fusobacterium sp. 3_1_5R 911 ACDD01000078 clade_470 N N Fusobacterium sp. D12 918 ACDG02000036 clade_470 N N Fusobacterium ulcerans 921 ACDH01000090 clade_470 N N Fusobacterium varium 922 ACIE01000009 clade_470 N N Mycoplasma arthritidis 1312 NC_011025 clade_473 N N Mycoplasma faucium 1314 NR_024983 clade_473 N N Mycoplasma hominis 1318 AF443616 clade_473 N N Mycoplasma orale 1319 AY796060 clade_473 N N Mycoplasma salivarium 1324 M24661 clade_473 N N Mitsuokella jalaludinii 1247 NR_028840 clade_474 N N Mitsuokella multacida 1248 ABWK02000005 clade_474 N N Mitsuokella sp. oral taxon 521 1249 GU413658 clade_474 N N Mitsuokella sp. oral taxon G68 1250 GU432166 clade_474 N N Selenomonas genomosp. C1 1695 AY278627 clade_474 N N Selenomonas genomosp. P8 oral clone MB5_P06 1700 DQ003628 clade_474 N N Selenomonas ruminantium 1703 NR_075026 clade_474 N N Veillonellaceae bacterium oral taxon 131 1994 GU402916 clade_474 N N Alloscardovia omnicolens 139 NR_042583 clade_475 N N Alloscardovia sp. OB7196 140 AB425070 clade_475 N N Bifidobacterium urinalis 366 AJ278695 clade_475 N N Eubacterium nodatum 854 U13041 clade_476 Y N Eubacterium saphenum 859 NR_026031 clade_476 Y N Eubacterium sp. oral clone JH012 867 AY349373 clade_476 Y N Eubacterium sp. oral clone JS001 870 AY349378 clade_476 Y N Faecalibacterium prausnitzii 880 ACOP02000011 clade_478 Y N Gemmiger formicilis 932 GU562446 clade_478 Y N Subdoligranulum variabile 1896 AJ518869 clade_478 Y N Clostridiaceae bacterium JC13 532 JF824807 clade_479 Y N Clostridium sp. MLG055 634 AF304435 clade_479 Y N Erysipelotrichaceae bacterium 3_1_53 822 ACTJ01000113 clade_479 Y N Prevotella loescheii 1503 JN867231 clade_48 N N Prevotella sp. oral clone ASCG12 1530 DQ272511 clade_48 N N Prevotella sp. oral clone GU027 1540 AY349398 clade_48 N N Prevotella sp. oral taxon 472 1553 ACZS01000106 clade_48 N N Selenomonas dianae 1693 GQ422719 clade_480 N N Selenomonas flueggei 1694 AF287803 clade_480 N N Selenomonas genomosp. C2 1696 AY278628 clade_480 N N Selenomonas genomosp. P6 oral clone MB3_C41 1698 DQ003636 clade_480 N N Selenomonas genomosp. P7 oral clone MB5_C08 1699 DQ003627 clade_480 N N Selenomonas infelix 1701 AF287802 clade_480 N N Selenomonas noxia 1702 GU470909 clade_480 N N Selenomonas sp. oral clone FT050 1705 AY349403 clade_480 N N Selenomonas sp. oral clone GI064 1706 AY349404 clade_480 N N Selenomonas sp. oral clone GT010 1707 AY349405 clade_480 N N Selenomonas sp. oral clone HU051 1708 AY349406 clade_480 N N Selenomonas sp. oral clone IK004 1709 AY349407 clade_480 N N Selenomonas sp. oral clone JI021 1711 AY349409 clade_480 N N Selenomonas sp. oral clone JS031 1712 AY349410 clade_480 N N Selenomonas sp. oral clone OH4A 1713 AY947498 clade_480 N N Selenomonas sp. oral clone P2PA_80 P4 1714 AY207052 clade_480 N N Selenomonas sp. oral taxon 149 1716 AEEJ01000007 clade_480 N N Veillonellaceae bacterium oral taxon 155 1995 GU470897 clade_480 N N Clostridium cocleatum 575 NR_026495 clade_481 Y N Clostridium ramosum 617 M23731 clade_481 Y N Clostridium saccharogumia 619 DQ100445 clade_481 Y N Clostridium spiroforme 644 X73441 clade_481 Y N Coprobacillus sp. D7 672 ACDT01000199 clade_481 Y N Clostridiales bacterium SY8519 535 AB477431 clade_482 Y N Clostridium sp. SY8519 639 AP012212 clade_482 Y N Eubacterium ramulus 855 AJ011522 clade_482 Y N Agrococcus jenensis 117 NR_026275 clade_484 N N Microbacterium gubbeenense 1232 NR_025098 clade_484 N N Pseudoclavibacter sp. Timone 1590 FJ375951 clade_484 N N Tropheryma whipplei 1961 BX251412 clade_484 N N Zimmermannella bifida 2031 AB012592 clade_484 N N Erysipelothrix inopinata 819 NR_025594 clade_485 Y N Erysipelothrix rhusiopathiae 820 ACLK01000021 clade_485 Y N Erysipelothrix tonsillarum 821 NR_040871 clade_485 Y N Holdemania filiformis 1004 Y11466 clade_485 Y N Mollicutes bacterium pACH93 1258 AY297808 clade_485 Y N Coxiella burnetii 736 CP000890 clade_486 Y Category- B Legionella hackeliae 1151 M36028 clade_486 N OP Legionella longbeachae 1152 M36029 clade_486 N OP Legionella sp. D3923 1154 JN380999 clade_486 N OP Legionella sp. D4088 1155 JN381012 clade_486 N OP Legionella sp. H63 1156 JF831047 clade_486 N OP Legionella sp. NML 93L054 1157 GU062706 clade_486 N OP Legionella steelei 1158 HQ398202 clade_486 N OP Tatlockia micdadei 1915 M36032 clade_486 N N Clostridium hiranonis 591 AB023970 clade_487 Y N Clostridium irregulare 596 NR_029249 clade_487 Y N Helicobacter pullorum 996 ABQU01000097 clade_489 N N Acetobacteraceae bacterium AT_5844 16 AGEZ01000040 clade_490 N N Roseomonas cervicalis 1643 ADVL01000363 clade_490 N N Roseomonas mucosa 1644 NR_028857 clade_490 N N Roseomonas sp. NML94_0193 1645 AF533357 clade_490 N N Roseomonas sp. NML97_0121 1646 AF533359 clade_490 N N Roseomonas sp. NML98_0009 1647 AF533358 clade_490 N N Roseomonas sp. NML98_0157 1648 AF533360 clade_490 N N Rickettsia akari 1627 CP000847 clade_492 N OP Rickettsia conorii 1628 AE008647 clade_492 N OP Rickettsia prowazekii 1629 M21789 clade_492 N Category- B Rickettsia rickettsii 1630 NC_010263 clade_492 N OP Rickettsia slovaca 1631 L36224 clade_492 N OP Rickettsia typhi 1632 AE017197 clade_492 N OP Anaeroglobus geminatus 160 AGCJ01000054 clade_493 N N Megasphaera genomosp. C1 1201 AY278622 clade_493 N N Megasphaera micronuciformis 1203 AECS01000020 clade_493 N N Clostridium orbiscindens 609 Y18187 clade_494 Y N Clostridium sp. NML 04A032 637 EU815224 clade_494 Y N Flavonifractor plautii 886 AY724678 clade_494 Y N Pseudoflavonifractor capillosus 1591 AY136666 clade_494 Y N Ruminococcaceae bacterium D16 1655 ADDX01000083 clade_494 Y N Acetivibrio cellulolyticus 5 NR_025917 clade_495 Y N Clostridiales genomosp. BVAB3 540 CP001850 clade_495 N N Clostridium aldrichii 548 NR_026099 clade_495 Y N Clostridium clariflavum 570 NR_041235 clade_495 Y N Clostridium stercorarium 647 NR_025100 clade_495 Y N Clostridium straminisolvens 649 NR_024829 clade_495 Y N Clostridium thermocellum 655 NR_074629 clade_495 Y N Tsukamurella paurometabola 1963 X80628 clade_496 N N Tsukamurella tyrosinosolvens 1964 AB478958 clade_496 N N Abiotrophia para_adiacens 2 AB022027 clade_497 N N Carnobacterium divergens 492 NR_044706 clade_497 N N Carnobacterium maltaromaticum 493 NC_019425 clade_497 N N Enterococcus avium 800 AF133535 clade_497 N N Enterococcus caccae 801 AY943820 clade_497 N N Enterococcus casseliflavus 802 AEWT01000047 clade_497 N N Enterococcus durans 803 AJ276354 clade_497 N N Enterococcus faecalis 804 AE016830 clade_497 N N Enterococcus faecium 805 AM157434 clade_497 N N Enterococcus gallinarum 806 AB269767 clade_497 N N Enterococcus gilvus 807 AY033814 clade_497 N N Enterococcus hawaiiensis 808 AY321377 clade_497 N N Enterococcus hirae 809 AF061011 clade_497 N N Enterococcus italicus 810 AEPV01000109 clade_497 N N Enterococcus mundtii 811 NR_024906 clade_497 N N Enterococcus raffinosus 812 FN600541 clade_497 N N Enterococcus sp. BV2CASA2 813 JN809766 clade_497 N N Enterococcus sp. CCRI 16620 814 GU457263 clade_497 N N Enterococcus sp. F95 815 FJ463817 clade_497 N N Enterococcus sp. RfL6 816 AJ133478 clade_497 N N Enterococcus thailandicus 817 AY321376 clade_497 N N Fusobacterium canifelinum 893 AY162222 clade_497 N N Fusobacterium genomosp. C1 894 AY278616 clade_497 N N Fusobacterium genomosp. C2 895 AY278617 clade_497 N N Fusobacterium nucleatum 901 ADVK01000034 clade_497 Y N Fusobacterium periodonticum 902 ACJY01000002 clade_497 N N Fusobacterium sp. 1_1_41FAA 906 ADGG01000053 clade_497 N N Fusobacterium sp. 11_3_2 904 ACUO01000052 clade_497 N N Fusobacterium sp. 2_1_31 907 ACDC02000018 clade_497 N N Fusobacterium sp. 3_1_27 908 ADGF01000045 clade_497 N N Fusobacterium sp. 3_1_33 909 ACQE01000178 clade_497 N N Fusobacterium sp. 3_1_36A2 910 ACPU01000044 clade_497 N N Fusobacterium sp. AC18 912 HQ616357 clade_497 N N Fusobacterium sp. ACB2 913 HQ616358 clade_497 N N Fusobacterium sp. AS2 914 HQ616361 clade_497 N N Fusobacterium sp. CM1 915 HQ616371 clade_497 N N Fusobacterium sp. CM21 916 HQ616375 clade_497 N N Fusobacterium sp. CM22 917 HQ616376 clade_497 N N Fusobacterium sp. oral clone ASCF06 919 AY923141 clade_497 N N Fusobacterium sp. oral clone ASCF11 920 AY953256 clade_497 N N Granulicatella adiacens 959 ACKZ01000002 clade_497 N N Granulicatella elegans 960 AB252689 clade_497 N N Granulicatella paradiacens 961 AY879298 clade_497 N N Granulicatella sp. oral clone ASC02 963 AY923126 clade_497 N N Granulicatella sp. oral clone ASCA05 964 DQ341469 clade_497 N N Granulicatella sp. oral clone ASCB09 965 AY953251 clade_497 N N Granulicatella sp. oral clone ASCG05 966 AY923146 clade_497 N N Tetragenococcus halophilus 1918 NR_075020 clade_497 N N Tetragenococcus koreensis 1919 NR_043113 clade_497 N N Vagococcus fluvialis 1973 NR_026489 clade_497 N N Chryseobacterium anthropi 514 AM982793 clade_498 N N Chryseobacterium gleum 515 ACKQ02000003 clade_498 N N Chryseobacterium hominis 516 NR_042517 clade_498 N N Treponema refringens 1936 AF426101 clade_499 N OP Treponema sp. oral clone JU031 1941 AY349416 clade_499 N N Treponema sp. oral taxon 239 1948 GU408738 clade_499 N N Treponema sp. oral taxon 271 1955 GU408871 clade_499 N N Alistipes finegoldii 129 NR_043064 clade_500 N N Alistipes onderdonkii 131 NR_043318 clade_500 N N Alistipes putredinis 132 ABFK02000017 clade_500 N N Alistipes shahii 133 FP929032 clade_500 N N Alistipes sp. HGB5 134 AENZ01000082 clade_500 N N Alistipes sp. JC50 135 JF824804 clade_500 N N Alistipes sp. RMA 9912 136 GQ140629 clade_500 N N Mycoplasma agalactiae 1310 AF010477 clade_501 N N Mycoplasma bovoculi 1313 NR_025987 clade_501 N N Mycoplasma fermentans 1315 CP002458 clade_501 N N Mycoplasma flocculare 1316 X62699 clade_501 N N Mycoplasma ovipneumoniae 1320 NR_025989 clade_501 N N Arcobacter butzleri 176 AEPT01000071 clade_502 N N Arcobacter cryaerophilus 177 NR_025905 clade_502 N N Campylobacter curvus 461 NC_009715 clade_502 N OP Campylobacter rectus 467 ACFU01000050 clade_502 N OP Campylobacter showae 468 ACVQ01000030 clade_502 N OP Campylobacter sp. FOBRC14 469 HQ616379 clade_502 N OP Campylobacter sp. FOBRC15 470 HQ616380 clade_502 N OP Campylobacter sp. oral clone BB120 471 AY005038 clade_502 N OP Campylobacter sputorum 472 NR_044839 clade_502 N OP Bacteroides ureolyticus 330 GQ167666 clade_504 N N Campylobacter gracilis 463 ACYG01000026 clade_504 N OP Campylobacter hominis 464 NC_009714 clade_504 N OP Dialister invisus 762 ACIM02000001 clade_506 N N Dialister micraerophilus 763 AFBB01000028 clade_506 N N Dialister microaerophilus 764 AENT01000008 clade_506 N N Dialister propionicifaciens 766 NR_043231 clade_506 N N Dialister succinatiphilus 768 AB370249 clade_506 N N Megasphaera elsdenii 1200 AY038996 clade_506 N N Megasphaera genomosp. type_1 1202 ADGP01000010 clade_506 N N Megasphaera sp. BLPYG_07 1204 HM990964 clade_506 N N Megasphaera sp. UPII 199_6 1205 AFIJ01000040 clade_506 N N Chromobacterium violaceum 513 NC_005085 clade_507 N N Laribacter hongkongensis 1148 CP001154 clade_507 N N Methylophilus sp. ECd5 1229 AY436794 clade_507 N N Finegoldia magna 883 ACHM02000001 clade_509 N N Parvimonas micra 1431 AB729072 clade_509 N N Parvimonas sp. oral taxon 110 1432 AFII01000002 clade_509 N N Peptostreptococcus micros 1456 AM176538 clade_509 N N Peptostreptococcus sp. oral clone FJ023 1460 AY349390 clade_509 N N Peptostreptococcus sp. P4P_31 P3 1458 AY207059 clade_509 N N Helicobacter pylori 997 CP000012 clade_510 N OP Anaplasma marginale 165 ABOR01000019 clade_511 N N Anaplasma phagocytophilum 166 NC_007797 clade_511 N N Ehrlichia chaffeensis 783 AAIF01000035 clade_511 N OP Neorickettsia risticii 1349 CP001431 clade_511 N N Neorickettsia sennetsu 1350 NC_007798 clade_511 N N Eubacterium barkeri 834 NR_044661 clade_512 Y N Eubacterium callanderi 838 NR_026330 clade_512 Y N Eubacterium limosum 850 CP002273 clade_512 Y N Pseudoramibacter alactolyticus 1606 AB036759 clade_512 N N Veillonella montpellierensis 1977 AF473836 clade_513 N N Veillonella sp. oral clone ASCA08 1988 AY923118 clade_513 N N Veillonella sp. oral clone ASCB03 1989 AY923122 clade_513 N N Inquilinus limosus 1012 NR_029046 clade_514 N N Sphingomonas sp. oral clone FZ016 1746 AY349412 clade_514 N N Anaerococcus lactolyticus 145 ABYO01000217 clade_515 N N Anaerococcus prevotii 147 CP001708 clade_515 N N Anaerococcus sp. gpac104 152 AM176528 clade_515 N N Anaerococcus sp. gpac126 153 AM176530 clade_515 N N Anaerococcus sp. gpac155 154 AM176536 clade_515 N N Anaerococcus sp. gpac199 155 AM176539 clade_515 N N Anaerococcus tetradius 157 ACGC01000107 clade_515 N N Bacteroides coagulans 271 AB547639 clade_515 N N Clostridiales bacterium 9403326 534 HM587324 clade_515 N N Clostridiales bacterium ph2 539 JN837487 clade_515 N N Peptostreptococcus sp. 9succ1 1457 X90471 clade_515 N N Peptostreptococcus sp. oral clone AP24 1459 AB175072 clade_515 N N Tissierella praeacuta 1924 NR_044860 clade_515 N N Anaerotruncus colihominis 164 ABGD02000021 clade_516 Y N Clostridium methylpentosum 606 ACEC01000059 clade_516 Y N Clostridium sp. YIT 12070 642 AB491208 clade_516 Y N Hydrogenoanaerobacterium saccharovorans 1005 NR_044425 clade_516 Y N Ruminococcus albus 1656 AY445600 clade_516 Y N Ruminococcus flavefaciens 1660 NR_025931 clade_516 Y N Clostridium haemolyticum 589 NR_024749 clade_517 Y N Clostridium novyi 608 NR_074343 clade_517 Y N Clostridium sp. LMG 16094 632 X95274 clade_517 Y N Helicobacter canadensis 994 ABQS01000108 clade_518 N N Eubacterium ventriosum 874 L34421 clade_519 Y N Peptostreptococcus anaerobius 1455 AY326462 clade_520 N N Peptostreptococcus stomatis 1461 ADGQ01000048 clade_520 N N Bilophila wadsworthia 367 ADCP01000166 clade_521 N N Desulfovibrio vulgaris 761 NR_074897 clade_521 N N Bacteroides galacturonicus 280 DQ497994 clade_522 Y N Eubacterium eligens 845 CP001104 clade_522 Y N Lachnospira multipara 1046 FR733699 clade_522 Y N Lachnospira pectinoschiza 1047 L14675 clade_522 Y N Lactobacillus rogosae 1114 GU269544 clade_522 Y N Actinomyces nasicola 64 AJ508455 clade_523 N N Cellulosimicrobium funkei 500 AY501364 clade_523 N N Lactococcus raffinolactis 1146 NR_044359 clade_524 N N Bacillus horti 214 NR_036860 clade_527 Y OP Bacillus sp. 9_3AIA 232 FN397519 clade_527 Y OP Bacteroidales genomosp. P1 258 AY341819 clade_529 N N Bacteroidales genomosp. P2 oral clone MB1_G13 259 DQ003613 clade_529 N N Bacteroidales genomosp. P3 oral clone MB1_G34 260 DQ003615 clade_529 N N Bacteroidales genomosp. P4 oral clone MB2_G17 261 DQ003617 clade_529 N N Bacteroidales genomosp. P5 oral clone MB2_P04 262 DQ003619 clade_529 N N Bacteroidales genomosp. P6 oral clone MB3_C19 263 DQ003634 clade_529 N N Bacteroidales genomosp. P8 oral clone MB4_G15 265 DQ003626 clade_529 N N Bacteroidetes bacterium oral taxon D27 333 HM099638 clade_530 N N Bacteroidetes bacterium oral taxon F31 334 HM099643 clade_530 N N Bacteroidetes bacterium oral taxon F44 335 HM099649 clade_530 N N Flavobacterium sp. NF2_1 885 FJ195988 clade_530 N N Myroides odoratimimus 1326 NR_042354 clade_530 N N Myroides sp. MY15 1327 GU253339 clade_530 N N Chlamydiales bacterium NS16 507 JN606076 clade_531 N N Chlamydophila pecorum 508 D88317 clade_531 N OP Parachlamydia sp. UWE25 1423 BX908798 clade_531 N N Fusobacterium russii 903 NR_044687 clade_532 N N Streptobacillus moniliformis 1784 NR_027615 clade_532 N N Eubacteriaceae bacterium P4P_50 P4 833 AY207060 clade_533 N N Eubacterium brachy 836 U13038 clade_533 Y N Filifactor alocis 881 CP002390 clade_533 Y N Filifactor villosus 882 NR_041928 clade_533 Y N Abiotrophia defectiva 1 ACIN02000016 clade_534 N N Abiotrophia sp. oral clone P4PA_155 P1 3 AY207063 clade_534 N N Catonella genomosp. P1 oral clone MB5_P12 496 DQ003629 clade_534 N N Catonella morbi 497 ACIL02000016 clade_534 N N Catonella sp. oral clone FL037 498 AY349369 clade_534 N N Eremococcus coleocola 818 AENN01000008 clade_534 N N Facklamia hominis 879 Y10772 clade_534 N N Granulicatella sp. M658_99_3 962 AJ271861 clade_534 N N Campylobacter coli 459 AAFL01000004 clade_535 N OP Campylobacter concisus 460 CP000792 clade_535 N OP Campylobacter fetus 462 ACLG01001177 clade_535 N OP Campylobacter jejuni 465 AL139074 clade_535 N Category- B Campylobacter upsaliensis 473 AEPU01000040 clade_535 N OP Clostridium leptum 601 AJ305238 clade_537 Y N Clostridium sp. YIT 12069 641 AB491207 clade_537 Y N Clostridium sporosphaeroides 646 NR_044835 clade_537 Y N Eubacterium coprostanoligenes 841 HM037995 clade_537 Y N Ruminococcus bromii 1657 EU266549 clade_537 Y N Eubacterium siraeum 860 ABCA03000054 clade_538 Y N Atopobium minutum 183 HM007583 clade_539 N N Atopobium parvulum 184 CP001721 clade_539 N N Atopobium rimae 185 ACFE01000007 clade_539 N N Atopobium sp. BS2 186 HQ616367 clade_539 N N Atopobium sp. F0209 187 EU592966 clade_539 N N Atopobium sp. ICM42b10 188 HQ616393 clade_539 N N Atopobium sp. ICM57 189 HQ616400 clade_539 N N Atopobium vaginae 190 AEDQ01000024 clade_539 N N Coriobacteriaceae bacterium BV3Ac1 677 JN809768 clade_539 N N Actinomyces naeslundii 63 X81062 clade_54 N N Actinomyces oricola 67 NR_025559 clade_54 N N Actinomyces oris 69 BABV01000070 clade_54 N N Actinomyces sp. 7400942 70 EU484334 clade_54 N N Actinomyces sp. ChDC B197 72 AF543275 clade_54 N N Actinomyces sp. GEJ15 73 GU561313 clade_54 N N Actinomyces sp. M2231_94_1 79 AJ234063 clade_54 N N Actinomyces sp. oral clone GU067 83 AY349362 clade_54 N N Actinomyces sp. oral clone IO077 85 AY349364 clade_54 N N Actinomyces sp. oral clone IP073 86 AY349365 clade_54 N N Actinomyces sp. oral clone JA063 88 AY349367 clade_54 N N Actinomyces sp. oral taxon 170 89 AFBL01000010 clade_54 N N Actinomyces sp. oral taxon 171 90 AECW01000034 clade_54 N N Actinomyces urogenitalis 95 ACFH01000038 clade_54 N N Actinomyces viscosus 96 ACRE01000096 clade_54 N N Clostridium viride 657 NR_026204 clade_540 Y N Oscillibacter sp. G2 1386 HM626173 clade_540 Y N Oscillibacter valericigenes 1387 NR_074793 clade_540 Y N Oscillospira guilliermondii 1388 AB040495 clade_540 Y N Orientia tsutsugamushi 1383 AP008981 clade_541 N OP Megamonas funiformis 1198 AB300988 clade_542 N N Megamonas hypermegale 1199 AJ420107 clade_542 N N Butyrivibrio crossotus 455 ABWN01000012 clade_543 Y N Clostridium sp. L2_50 631 AAYW02000018 clade_543 Y N Coprococcus eutactus 675 EF031543 clade_543 Y N Coprococcus sp. ART55_1 676 AY350746 clade_543 Y N Eubacterium ruminantium 857 NR_024661 clade_543 Y N Aeromicrobium marinum 102 NR_025681 clade_544 N N Aeromicrobium sp. JC14 103 JF824798 clade_544 N N Luteococcus sanguinis 1190 NR_025507 clade_544 N N Propionibacteriaceae bacterium NML 02_0265 1568 EF599122 clade_544 N N Rhodococcus corynebacterioides 1622 X80615 clade_546 N N Rhodococcus erythropolis 1624 ACNO01000030 clade_546 N N Rhodococcus fascians 1625 NR_037021 clade_546 N N Segniliparus rotundus 1690 CP001958 clade_546 N N Segniliparus rugosus 1691 ACZI01000025 clade_546 N N Exiguobacterium acetylicum 878 FJ970034 clade_547 N N Macrococcus caseolyticus 1194 NR_074941 clade_547 N N Streptomyces sp. 1 AIP_2009 1890 FJ176782 clade_548 N N Streptomyces sp. SD 524 1892 EU544234 clade_548 N N Streptomyces sp. SD 528 1893 EU544233 clade_548 N N Streptomyces thermoviolaceus 1895 NR_027616 clade_548 N N Borrelia afzelii 388 ABCU01000001 clade_549 N OP Borrelia crocidurae 390 DQ057990 clade_549 N OP Borrelia duttonii 391 NC_011229 clade_549 N OP Borrelia hermsii 393 AY597657 clade_549 N OP Borrelia hispanica 394 DQ057988 clade_549 N OP Borrelia persica 395 HM161645 clade_549 N OP Borrelia recurrentis 396 AF107367 clade_549 N OP Borrelia spielmanii 398 ABKB01000002 clade_549 N OP Borrelia turicatae 399 NC_008710 clade_549 N OP Borrelia valaisiana 400 ABCY01000002 clade_549 N OP Providencia alcalifaciens 1586 ABXW01000071 clade_55 N N Providencia rettgeri 1587 AM040492 clade_55 N N Providencia rustigianii 1588 AM040489 clade_55 N N Providencia stuartii 1589 AF008581 clade_55 N N Treponema pallidum 1932 CP001752 clade_550 N OP Treponema phagedenis 1934 AEFH01000172 clade_550 N N Treponema sp. clone DDKL_4 1939 Y08894 clade_550 N N Acholeplasma laidlawii 17 NR_074448 clade_551 N N Mycoplasma putrefaciens 1323 U26055 clade_551 N N Mycoplasmataceae genomosp P1 oral clone 1325 DQ003614 clade_551 N N Spiroplasma insolitum 1750 NR_025705 clade_551 N N Collinsella aerofaciens 659 AAVN02000007 clade_553 Y N Collinsella intestinalis 660 ABXH02000037 clade_553 N N Collinsella stercoris 661 ABXJ01000150 clade_553 N N Collinsella tanakaei 662 AB490807 clade_553 N N Alkaliphilus metalliredigenes 137 AY137848 clade_554 Y N Alkaliphilus oremlandii 138 NR_043674 clade_554 Y N Caminicella sporogenes 458 NR_025485 clade_554 N N Clostridium sticklandii 648 L04167 clade_554 Y N Turicibacter sanguinis 1965 AF349724 clade_555 Y N Acidaminococcus fermentans 21 CP001859 clade_556 N N Acidaminococcus intestini 22 CP003058 clade_556 N N Acidaminococcus sp. D21 23 ACGB01000071 clade_556 N N Phascolarctobacterium faecium 1462 NR_026111 clade_556 N N Phascolarctobacterium sp. YIT 12068 1463 AB490812 clade_556 N N Phascolarctobacterium succinatutens 1464 AB490811 clade_556 N N Acidithiobacillus ferrivorans 25 NR_074660 clade_557 N N Fulvimonas sp. NML 060897 892 EF589680 clade_557 Y N Xanthomonadaceae bacterium NML 03_0222 2015 EU313791 clade_557 N N Catabacter hongkongensis 494 AB671763 clade_558 N N Christensenella minuta 512 AB490809 clade_558 N N Clostridiales bacterium oral clone P4PA 536 AY207065 clade_558 N N Clostridiales bacterium oral taxon 093 537 GQ422712 clade_558 N N Desulfitobacterium frappieri 753 AJ276701 clade_560 Y N Desulfitobacterium hafniense 754 NR_074996 clade_560 Y N Desulfotomaculum nigrificans 756 NR_044832 clade_560 Y N Heliobacterium modesticaldum 1000 NR_074517 clade_560 N N Alistipes indistinctus 130 AB490804 clade_561 N N Bacteroidales bacterium ph8 257 JN837494 clade_561 N N Candidatus Sulcia muelleri 475 CP002163 clade_561 N N Cytophaga xylanolytica 742 FR733683 clade_561 N N Flavobacteriaceae genomosp. C1 884 AY278614 clade_561 N N Gramella forsetii 958 NR_074707 clade_561 N N Sphingobacterium faecium 1740 NR_025537 clade_562 N N Sphingobacterium mizutaii 1741 JF708889 clade_562 N N Sphingobacterium multivorum 1742 NR_040953 clade_562 N N Sphingobacterium spiritivorum 1743 ACHA02000013 clade_562 N N Jonquetella anthropi 1017 ACOO02000004 clade_563 N N Pyramidobacter piscolens 1614 AY207056 clade_563 N N Synergistes genomosp. C1 1904 AY278615 clade_563 N N Synergistes sp. RMA 14551 1905 DQ412722 clade_563 N N Synergistetes bacterium ADV897 1906 GQ258968 clade_563 N N Candidatus Arthromitus sp. SFB_mouse_Yit 474 NR_074460 clade_564 N N Gracilibacter thermotolerans 957 NR_043559 clade_564 N N Lutispora thermophila 1191 NR_041236 clade_564 Y N Brachyspira aalborgi 404 FM178386 clade_565 N N Brachyspira pilosicoli 405 NR_075069 clade_565 Y N Brachyspira sp. HIS3 406 FM178387 clade_565 N N Brachyspira sp. HIS4 407 FM178388 clade_565 N N Brachyspira sp. HIS5 408 FM178389 clade_565 N N Adlercreutzia equolifaciens 97 AB306661 clade_566 N N Coriobacteriaceae bacterium JC110 678 CAEM01000062 clade_566 N N Coriobacteriaceae bacterium phI 679 JN837493 clade_566 N N Cryptobacterium curtum 740 GQ422741 clade_566 N N Eggerthella lenta 778 AF292375 clade_566 Y N Eggerthella sinensis 779 AY321958 clade_566 N N Eggerthella sp. 1_3_56FAA 780 ACWN01000099 clade_566 N N Eggerthella sp. HGA1 781 AEXR01000021 clade_566 N N Eggerthella sp. YY7918 782 AP012211 clade_566 N N Gordonibacter pamelaeae 680 AM886059 clade_566 N N Gordonibacter pamelaeae 956 FP929047 clade_566 N N Slackia equolifaciens 1732 EU377663 clade_566 N N Slackia exigua 1733 ACUX01000029 clade_566 N N Slackia faecicanis 1734 NR_042220 clade_566 N N Slackia heliotrinireducens 1735 NR_074439 clade_566 N N Slackia isoflavoniconvertens 1736 AB566418 clade_566 N N Slackia piriformis 1737 AB490806 clade_566 N N Slackia sp. NATTS 1738 AB505075 clade_566 N N Streptomyces albus 1888 AJ697941 clade_566 Y N Chlamydiales bacterium NS11 505 JN606074 clade_567 Y N Chlamydiales bacterium NS13 506 JN606075 clade_567 N N Victivallaceae bacterium NML 080035 2003 FJ394915 clade_567 N N Victivallis vadensis 2004 ABDE02000010 clade_567 N N Anaerofustis stercorihominis 159 ABIL02000005 clade_570 Y N Butyricicoccus pullicaecorum 453 HH793440 clade_572 Y N Eubacterium desmolans 843 NR_044644 clade_572 Y N Papillibacter cinnamivorans 1415 NR_025025 clade_572 Y N Sporobacter termitidis 1751 NR_044972 clade_572 Y N Streptomyces griseus 1889 NR_074787 clade_573 N N Streptomyces sp. SD 511 1891 EU544231 clade_573 N N Streptomyces sp. SD 534 1894 EU544232 clade_573 N N Cloacibacillus evryensis 530 GQ258966 clade_575 N N Deferribacteres sp. oral clone JV001 743 AY349370 clade_575 N N Deferribacteres sp. oral clone JV006 744 AY349371 clade_575 Y N Deferribacteres sp. oral clone JV023 745 AY349372 clade_575 N N Synergistetes bacterium LBVCM1157 1907 GQ258969 clade_575 N N Synergistetes bacterium oral taxon 362 1909 GU410752 clade_575 N N Synergistetes bacterium oral taxon D48 1910 GU430992 clade_575 N N Clostridium colinum 577 NR_026151 clade_576 Y N Clostridium lactatifermentans 599 NR_025651 clade_576 Y N Clostridium piliforme 614 D14639 clade_576 Y N Peptococcus sp. oral clone JM048 1439 AY349389 clade_576 N N Helicobacter winghamensis 999 ACDO01000013 clade_577 N N Wolinella succinogenes 2014 BX571657 clade_577 N N Olsenella genomosp. C1 1368 AY278623 clade_578 N N Olsenella profusa 1369 FN178466 clade_578 N N Olsenella sp. F0004 1370 EU592964 clade_578 N N Olsenella sp. oral taxon 809 1371 ACVE01000002 clade_578 N N Olsenella uli 1372 CP002106 clade_578 N N Nocardiopsis dassonvillei 1356 CP002041 clade_579 N N Saccharomonospora viridis 1671 X54286 clade_579 Y N Thermobifida fusca 1921 NC_007333 clade_579 Y N Peptococcus niger 1438 NR_029221 clade_580 N N Peptococcus sp. oral taxon 167 1440 GQ422727 clade_580 N N Akkermansia muciniphila 118 CP001071 clade_583 N N Opitutus terrae 1373 NR_074978 clade_583 N N Clostridiales bacterium oral taxon F32 538 HM099644 clade_584 N N Leptospira borgpetersenii 1161 NC_008508 clade_585 N OP Leptospira broomii 1162 NR_043200 clade_585 N OP Leptospira interrogans 1163 NC_005823 clade_585 N OP Leptospira licerasiae 1164 EF612284 clade_585 Y OP Methanobrevibacter gottschalkii 1213 NR_044789 clade_587 N N Methanobrevibacter millerae 1214 NR_042785 clade_587 N N Methanobrevibacter oralis 1216 HE654003 clade_587 N N Methanobrevibacter thaueri 1219 NR_044787 clade_587 N N Methanobrevibacter smithii 1218 ABYV02000002 clade_588 N N Deinococcus radiodurans 746 AE000513 clade_589 N N Deinococcus sp. R_43890 747 FR682752 clade_589 N N Thermus aquaticus 1923 NR_025900 clade_589 N N Actinomyces sp. c109 81 AB167239 clade_590 N N Moorella thermoacetica 1259 NR_075001 clade_590 Y N Syntrophomonadaceae genomosp. P1 1912 AY341821 clade_590 N N Thermoanaerobacter pseudethanolicus 1920 CP000924 clade_590 Y N Anaerobaculum hydrogeniformans 141 ACJX02000009 clade_591 N N Flexistipes sinusarabici 888 NR_074881 clade_591 Y N Microcystis aeruginosa 1246 NC_010296 clade_592 N N Prochlorococcus marinus 1567 CP000551 clade_592 N N Methanobrevibacter acididurans 1208 NR_028779 clade_593 N N Methanobrevibacter arboriphilus 1209 NR_042783 clade_593 N N Methanobrevibacter curvatus 1210 NR_044796 clade_593 N N Methanobrevibacter cuticularis 1211 NR_044776 clade_593 N N Methanobrevibacter filiformis 1212 NR_044801 clade_593 N N Methanobrevibacter woesei 1220 NR_044788 clade_593 N N Roseiflexus castenholzii 1642 CP000804 clade_594 N N Methanobrevibacter olleyae 1215 NR_043024 clade_595 N N Methanobrevibacter ruminantium 1217 NR_042784 clade_595 N N Methanobrevibacter wolinii 1221 NR_044790 clade_595 N N Methanosphaera stadtmanae 1222 AY196684 clade_595 N N Chloroflexi genomosp. P1 511 AY331414 clade_596 N N Gloeobacter violaceus 942 NR_074282 clade_596 Y N Halorubrum lipolyticum 992 AB477978 clade_597 N N Methanobacterium formicicum 1207 NR_025028 clade_597 N N Acidilobus saccharovorans 24 AY350586 clade_598 N N Hyperthermus butylicus 1006 CP000493 clade_598 N N Ignicoccus islandicus 1011 X99562 clade_598 N N Metallosphaera sedula 1206 D26491 clade_598 N N Thermofilum pendens 1922 X14835 clade_598 N N Prevotella melaninogenica 1506 CP002122 clade_6 N N Prevotella sp. ICM1 1520 HQ616385 clade_6 N N Prevotella sp. oral clone FU048 1535 AY349393 clade_6 N N Prevotella sp. oral clone GI030 1537 AY349395 clade_6 N N Prevotella sp. SEQ116 1526 JN867246 clade_6 N N Streptococcus anginosus 1787 AECT01000011 clade_60 N N Streptococcus milleri 1812 X81023 clade_60 N N Streptococcus sp. 16362 1829 JN590019 clade_60 N N Streptococcus sp. 69130 1832 X78825 clade_60 N N Streptococcus sp. AC15 1833 HQ616356 clade_60 N N Streptococcus sp. CM7 1839 HQ616373 clade_60 N N Streptococcus sp. OBRC6 1847 HQ616352 clade_60 N N Burkholderia ambifaria 442 AAUZ01000009 clade_61 N OP Burkholderia cenocepacia 443 AAHI01000060 clade_61 N OP Burkholderia cepacia 444 NR_041719 clade_61 N OP Burkholderia mallei 445 CP000547 clade_61 N Category- B Burkholderia multivorans 446 NC_010086 clade_61 N OP Burkholderia oklahomensis 447 DQ108388 clade_61 N OP Burkholderia pseudomallei 448 CP001408 clade_61 N Category- B Burkholderia rhizoxinica 449 HQ005410 clade_61 N OP Burkholderia sp. 383 450 CP000151 clade_61 N OP Burkholderia xenovorans 451 U86373 clade_61 N OP Prevotella buccae 1488 ACRB01000001 clade_62 N N Prevotella genomosp. P8 oral clone MB3_P13 1498 DQ003622 clade_62 N N Prevotella sp. oral clone FW035 1536 AY349394 clade_62 N N Prevotella bivia 1486 ADFO01000096 clade_63 N N Prevotella disiens 1494 AEDO01000026 clade_64 N N Bacteroides faecis 276 GQ496624 clade_65 N N Bacteroides fragilis 279 AP006841 clade_65 N N Bacteroides nordii 285 NR_043017 clade_65 N N Bacteroides salyersiae 292 EU136690 clade_65 N N Bacteroides sp. 1_1_14 293 ACRP01000155 clade_65 N N Bacteroides sp. 1_1_6 295 ACIC01000215 clade_65 N N Bacteroides sp. 2_1_56FAA 298 ACWI01000065 clade_65 N N Bacteroides sp. AR29 316 AF139525 clade_65 N N Bacteroides sp. B2 317 EU722733 clade_65 N N Bacteroides thetaiotaomicron 328 NR_074277 clade_65 N N Actinobacillus minor 45 ACFT01000025 clade_69 N N Haemophilus parasuis 978 GU226366 clade_69 N N Vibrio cholerae 1996 AAUR01000095 clade_71 N Category- B Vibrio fluvialis 1997 X76335 clade_71 N Category- B Vibrio furnissii 1998 CP002377 clade_71 N Category- B Vibrio mimicus 1999 ADAF01000001 clade_71 N Category- B Vibrio parahaemolyticus 2000 AAWQ01000116 clade_71 N Category- B Vibrio sp. RC341 2001 ACZT01000024 clade_71 N Category- B Vibrio vulnificus 2002 AE016796 clade_71 N Category- B Lactobacillus acidophilus 1067 CP000033 clade_72 N N Lactobacillus amylolyticus 1069 ADNY01000006 clade_72 N N Lactobacillus amylovorus 1070 CP002338 clade_72 N N Lactobacillus crispatus 1078 ACOG01000151 clade_72 N N Lactobacillus delbrueckii 1080 CP002341 clade_72 N N Lactobacillus helveticus 1088 ACLM01000202 clade_72 N N Lactobacillus kalixensis 1094 NR_029083 clade_72 N N Lactobacillus kefiranofaciens 1095 NR_042440 clade_72 N N Lactobacillus leichmannii 1098 JX986966 clade_72 N N Lactobacillus sp. 66c 1120 FR681900 clade_72 N N Lactobacillus sp. KLDS 1.0701 1122 EU600905 clade_72 N N Lactobacillus sp. KLDS 1.0712 1130 EU600916 clade_72 N N Lactobacillus sp. oral clone HT070 1136 AY349383 clade_72 N N Lactobacillus ultunensis 1139 ACGU01000081 clade_72 N N Prevotella intermedia 1502 AF414829 clade_81 N N Prevotella nigrescens 1511 AFPX01000069 clade_81 N N Prevotella pallens 1515 AFPY01000135 clade_81 N N Prevotella sp. oral taxon 310 1551 GQ422737 clade_81 N N Prevotella genomosp. C1 1495 AY278624 clade_82 N N Prevotella sp. CM38 1519 HQ610181 clade_82 N N Prevotella sp. oral taxon 317 1552 ACQH01000158 clade_82 N N Prevotella sp. SG12 1527 GU561343 clade_82 N N Prevotella denticola 1493 CP002589 clade_83 N N Prevotella genomosp. P7 oral clone MB2_P31 1497 DQ003620 clade_83 N N Prevotella histicola 1501 JN867315 clade_83 N N Prevotella multiformis 1508 AEWX01000054 clade_83 N N Prevotella sp. JCM 6330 1522 AB547699 clade_83 N N Prevotella sp. oral clone GI059 1539 AY349397 clade_83 N N Prevotella sp. oral taxon 782 1555 GQ422745 clade_83 N N Prevotella sp. oral taxon G71 1559 GU432180 clade_83 N N Prevotella sp. SEQ065 1524 JN867234 clade_83 N N Prevotella veroralis 1565 ACVA01000027 clade_83 N N Bacteroides acidifaciens 266 NR_028607 clade_85 N N Bacteroides cellulosilyticus 269 ACCH01000108 clade_85 N N Bacteroides clarus 270 AFBM01000011 clade_85 N N Bacteroides eggerthii 275 ACWG01000065 clade_85 N N Bacteroides oleiciplenus 286 AB547644 clade_85 N N Bacteroides pyogenes 290 NR_041280 clade_85 N N Bacteroides sp. 315_5 300 FJ848547 clade_85 N N Bacteroides sp. 31SF15 301 AJ583248 clade_85 N N Bacteroides sp. 31SF18 302 AJ583249 clade_85 N N Bacteroides sp. 35AE31 303 AJ583244 clade_85 N N Bacteroides sp. 35AE37 304 AJ583245 clade_85 N N Bacteroides sp. 35BE34 305 AJ583246 clade_85 N N Bacteroides sp. 35BE35 306 AJ583247 clade_85 N N Bacteroides sp. WH2 324 AY895180 clade_85 N N Bacteroides sp. XB12B 325 AM230648 clade_85 N N Bacteroides stercoris 327 ABFZ02000022 clade_85 N N Actinobacillus pleuropneumoniae 46 NR_074857 clade_88 N N Actinobacillus ureae 48 AEVG01000167 clade_88 N N Haemophilus aegyptius 969 AFBC01000053 clade_88 N N Haemophilus ducreyi 970 AE017143 clade_88 N OP Haemophilus haemolyticus 973 JN175335 clade_88 N N Haemophilus influenzae 974 AADP01000001 clade_88 N OP Haemophilus parahaemolyticus 975 GU561425 clade_88 N N Haemophilus parainfluenzae 976 AEWU01000024 clade_88 N N Haemophilus paraphrophaemolyticus 977 M75076 clade_88 N N Haemophilus somnus 979 NC_008309 clade_88 N N Haemophilus sp. 70334 980 HQ680854 clade_88 N N Haemophilus sp. HK445 981 FJ685624 clade_88 N N Haemophilus sp. oral clone ASCA07 982 AY923117 clade_88 N N Haemophilus sp. oral clone ASCG06 983 AY923147 clade_88 N N Haemophilus sp. oral clone BJ021 984 AY005034 clade_88 N N Haemophilus sp. oral clone BJ095 985 AY005033 clade_88 N N Haemophilus sp. oral taxon 851 987 AGRK01000004 clade_88 N N Haemophilus sputorum 988 AFNK01000005 clade_88 N N Histophilus somni 1003 AF549387 clade_88 N N Mannheimia haemolytica 1195 ACZX01000102 clade_88 N N Pasteurella bettyae 1433 L06088 clade_88 N N Moellerella wisconsensis 1253 JN175344 clade_89 N N Morganella morganii 1265 AJ301681 clade_89 N N Morganella sp. JB_T16 1266 AJ781005 clade_89 N N Proteus mirabilis 1582 ACLE01000013 clade_89 N N Proteus penneri 1583 ABVP01000020 clade_89 N N Proteus sp. HS7514 1584 DQ512963 clade_89 N N Proteus vulgaris 1585 AJ233425 clade_89 N N Eubacterium sp. oral clone JN088 869 AY349377 clade_90 Y N Oribacterium sinus 1374 ACKX01000142 clade_90 N N Oribacterium sp. ACB1 1375 HM120210 clade_90 N N Oribacterium sp. ACB7 1376 HM120211 clade_90 N N Oribacterium sp. CM12 1377 HQ616374 clade_90 N N Oribacterium sp. ICM51 1378 HQ616397 clade_90 N N Oribacterium sp. OBRC12 1379 HQ616355 clade_90 N N Oribacterium sp. oral taxon 108 1382 AFIH01000001 clade_90 N N Actinobacillus actinomycetemcomitans 44 AY362885 clade_92 N N Actinobacillus succinogenes 47 CP000746 clade_92 N N Aggregatibacter actinomycetemcomitans 112 CP001733 clade_92 N N Aggregatibacter aphrophilus 113 CP001607 clade_92 N N Aggregatibacter segnis 114 AEPS01000017 clade_92 N N Averyella dalhousiensis 194 DQ481464 clade_92 N N Bisgaard Taxon 368 AY683487 clade_92 N N Bisgaard Taxon 369 AY683489 clade_92 N N Bisgaard Taxon 370 AY683491 clade_92 N N Bisgaard Taxon 371 AY683492 clade_92 N N Buchnera aphidicola 440 NR_074609 clade_92 N N Cedecea davisae 499 AF493976 clade_92 N N Citrobacter amalonaticus 517 FR870441 clade_92 N N Citrobacter braakii 518 NR_028687 clade_92 N N Citrobacter farmeri 519 AF025371 clade_92 N N Citrobacter freundii 520 NR_028894 clade_92 N N Citrobacter gillenii 521 AF025367 clade_92 N N Citrobacter koseri 522 NC_009792 clade_92 N N Citrobacter murliniae 523 AF025369 clade_92 N N Citrobacter rodentium 524 NR_074903 clade_92 N N Citrobacter sedlakii 525 AF025364 clade_92 N N Citrobacter sp. 30_2 526 ACDJ01000053 clade_92 N N Citrobacter sp. KMSI_3 527 GQ468398 clade_92 N N Citrobacter werkmanii 528 AF025373 clade_92 N N Citrobacter youngae 529 ABWL02000011 clade_92 N N Cronobacter malonaticus 737 GU122174 clade_92 N N Cronobacter sakazakii 738 NC_009778 clade_92 N N Cronobacter turicensis 739 FN543093 clade_92 N N Enterobacter aerogenes 786 AJ251468 clade_92 N N Enterobacter asburiae 787 NR_024640 clade_92 N N Enterobacter cancerogenus 788 Z96078 clade_92 N N Enterobacter cloacae 789 FP929040 clade_92 N N Enterobacter cowanii 790 NR_025566 clade_92 N N Enterobacter hormaechei 791 AFHR01000079 clade_92 N N Enterobacter sp. 247BMC 792 HQ122932 clade_92 N N Enterobacter sp. 638 793 NR_074777 clade_92 N N Enterobacter sp. JC163 794 JN657217 clade_92 N N Enterobacter sp. SCSS 795 HM007811 clade_92 N N Enterobacter sp. TSE38 796 HM156134 clade_92 N N Enterobacteriaceae bacterium 9_2_54FAA 797 ADCU01000033 clade_92 N N Enterobacteriaceae bacterium CF01Ent_1 798 AJ489826 clade_92 N N Enterobacteriaceae bacterium Smarlab 3302238 799 AY538694 clade_92 N N Escherichia albertii 824 ABKX01000012 clade_92 N N Escherichia coli 825 NC_008563 clade_92 N Category- B Escherichia fergusonii 826 CU928158 clade_92 N N Escherichia hermannii 827 HQ407266 clade_92 N N Escherichia sp. 1_1_43 828 ACID01000033 clade_92 N N Escherichia sp. 4_1_40B 829 ACDM02000056 clade_92 N N Escherichia sp. B4 830 EU722735 clade_92 N N Escherichia vulneris 831 NR_041927 clade_92 N N Ewingella americana 877 JN175329 clade_92 N N Haemophilus genomosp. P2 oral clone MB3_C24 971 DQ003621 clade_92 N N Haemophilus genomosp. P3 oral clone MB3_C38 972 DQ003635 clade_92 N N Haemophilus sp. oral clone JM053 986 AY349380 clade_92 N N Hafnia alvei 989 DQ412565 clade_92 N N Klebsiella oxytoca 1024 AY292871 clade_92 N OP Klebsiella pneumoniae 1025 CP000647 clade_92 N OP Klebsiella sp. AS10 1026 HQ616362 clade_92 N N Klebsiella sp. Co9935 1027 DQ068764 clade_92 N N Klebsiella sp. enrichment culture clone SRC_DSD25 1036 HM195210 clade_92 N N Klebsiella sp. OBRC7 1028 HQ616353 clade_92 N N Klebsiella sp. SP_BA 1029 FJ999767 clade_92 N N Klebsiella sp. SRC_DSD1 1033 GU797254 clade_92 N N Klebsiella sp. SRC_DSD11 1030 GU797263 clade_92 N N Klebsiella sp. SRC_DSD12 1031 GU797264 clade_92 N N Klebsiella sp. SRC_DSD15 1032 GU797267 clade_92 N N Klebsiella sp. SRC_DSD2 1034 GU797253 clade_92 N N Klebsiella sp. SRC_DSD6 1035 GU797258 clade_92 N N Klebsiella variicola 1037 CP001891 clade_92 N N Kluyvera ascorbata 1038 NR_028677 clade_92 N N Kluyvera cryocrescens 1039 NR_028803 clade_92 N N Leminorella grimontii 1159 AJ233421 clade_92 N N Leminorella richardii 1160 HF558368 clade_92 N N Pantoea agglomerans 1409 AY335552 clade_92 N N Pantoea ananatis 1410 CP001875 clade_92 N N Pantoea brenneri 1411 EU216735 clade_92 N N Pantoea citrea 1412 EF688008 clade_92 N N Pantoea conspicua 1413 EU216737 clade_92 N N Pantoea septica 1414 EU216734 clade_92 N N Pasteurella dagmatis 1434 ACZR01000003 clade_92 N N Pasteurella multocida 1435 NC_002663 clade_92 N N Plesiomonas shigelloides 1469 X60418 clade_92 N N Raoultella ornithinolytica 1617 AB364958 clade_92 N N Raoultella planticola 1618 AF129443 clade_92 N N Raoultella terrigena 1619 NR_037085 clade_92 N N Salmonella bongori 1683 NR_041699 clade_92 N Category- B Salmonella enterica 1672 NC_011149 clade_92 N Category- B Salmonella enterica 1673 NC_011205 clade_92 N Category- B Salmonella enterica 1674 DQ344532 clade_92 N Category- B Salmonella enterica 1675 ABEH02000004 clade_92 N Category- B Salmonella enterica 1676 ABAK02000001 clade_92 N Category- B Salmonella enterica 1677 NC_011080 clade_92 N Category- B Salmonella enterica 1678 EU118094 clade_92 N Category- B Salmonella enterica 1679 NC_011094 clade_92 N Category- B Salmonella enterica 1680 AE014613 clade_92 N Category- B Salmonella enterica 1682 ABFH02000001 clade_92 N Category- B Salmonella enterica 1684 ABEM01000001 clade_92 N Category- B Salmonella enterica 1685 ABAM02000001 clade_92 N Category- B Salmonella typhimurium 1681 DQ344533 clade_92 N Category- B Salmonella typhimurium 1686 AF170176 clade_92 N Category- B Serratia fonticola 1718 NR_025339 clade_92 N N Serratia liquefaciens 1719 NR_042062 clade_92 N N Serratia marcescens 1720 GU826157 clade_92 N N Serratia odorifera 1721 ADBY01000001 clade_92 N N Serratia proteamaculans 1722 AAUN01000015 clade_92 N N Shigella boydii 1724 AAKA01000007 clade_92 N Category- B Shigella dysenteriae 1725 NC_007606 clade_92 N Category- B Shigella flexneri 1726 AE005674 clade_92 N Category- B Shigella sonnei 1727 NC_007384 clade_92 N Category- B Tatumella ptyseos 1916 NR_025342 clade_92 N N Trabulsiella guamensis 1925 AY373830 clade_92 N N Yersinia aldovae 2019 AJ871363 clade_92 N OP Yersinia aleksiciae 2020 AJ627597 clade_92 N OP Yersinia bercovieri 2021 AF366377 clade_92 N OP Yersinia enterocolitica 2022 FR729477 clade_92 N Category- B Yersinia frederiksenii 2023 AF366379 clade_92 N OP Yersinia intermedia 2024 AF366380 clade_92 N OP Yersinia kristensenii 2025 ACCA01000078 clade_92 N OP Yersinia mollaretii 2026 NR_027546 clade_92 N OP Yersinia pestis 2027 AE013632 clade_92 N Category- A Yersinia pseudotuberculosis 2028 NC_009708 clade_92 N OP Yersinia rohdei 2029 ACCD01000071 clade_92 N OP Yokenella regensburgei 2030 AB273739 clade_92 N N Conchiformibius kuhniae 669 NR_041821 clade_94 N N Morococcus cerebrosus 1267 JN175352 clade_94 N N Neisseria bacilliformis 1328 AFAY01000058 clade_94 N N Neisseria cinerea 1329 ACDY01000037 clade_94 N N Neisseria flavescens 1331 ACQV01000025 clade_94 N N Neisseria gonorrhoeae 1333 CP002440 clade_94 N OP Neisseria lactamica 1334 ACEQ01000095 clade_94 N N Neisseria macacae 1335 AFQE01000146 clade_94 N N Neisseria meningitidis 1336 NC_003112 clade_94 N OP Neisseria mucosa 1337 ACDX01000110 clade_94 N N Neisseria pharyngis 1338 AJ239281 clade_94 N N Neisseria polysaccharea 1339 ADBE01000137 clade_94 N N Neisseria sicca 1340 ACK002000016 clade_94 N N Neisseria sp. KEM232 1341 GQ203291 clade_94 N N Neisseria sp. oral clone AP132 1344 AY005027 clade_94 N N Neisseria sp. oral strain B33KA 1346 AY005028 clade_94 N N Neisseria sp. oral taxon 014 1347 ADEA01000039 clade_94 N N Neisseria sp. TM10_1 1343 DQ279352 clade_94 N N Neisseria subflava 1348 ACEO01000067 clade_94 N N Clostridium oroticum 610 FR749922 clade_96 Y N Clostridium sp. D5 627 ADBG01000142 clade_96 Y N Eubacterium contortum 840 FR749946 clade_96 Y N Eubacterium fissicatena 846 FR749935 clade_96 Y N Okadaella gastrococcus 1365 HQ699465 clade_98 N N Streptococcus agalactiae 1785 AAJO01000130 clade_98 N N Streptococcus alactolyticus 1786 NR_041781 clade_98 N N Streptococcus australis 1788 AEQR01000024 clade_98 N N Streptococcus bovis 1789 AEEL01000030 clade_98 N N Streptococcus canis 1790 AJ413203 clade_98 N N Streptococcus constellatus 1791 AY277942 clade_98 N N Streptococcus cristatus 1792 AEVC01000028 clade_98 N N Streptococcus dysgalactiae 1794 AP010935 clade_98 N N Streptococcus equi 1795 CP001129 clade_98 N N Streptococcus equinus 1796 AEVB01000043 clade_98 N N Streptococcus gallolyticus 1797 FR824043 clade_98 N N Streptococcus genomosp. C1 1798 AY278629 clade_98 N N Streptococcus genomosp. C2 1799 AY278630 clade_98 N N Streptococcus genomosp. C3 1800 AY278631 clade_98 N N Streptococcus genomosp. C4 1801 AY278632 clade_98 N N Streptococcus genomosp. C5 1802 AY278633 clade_98 N N Streptococcus genomosp. C6 1803 AY278634 clade_98 N N Streptococcus genomosp. C7 1804 AY278635 clade_98 N N Streptococcus genomosp. C8 1805 AY278609 clade_98 N N Streptococcus gordonii 1806 NC_009785 clade_98 N N Streptococcus infantarius 1807 ABJK02000017 clade_98 N N Streptococcus infantis 1808 AFNN01000024 clade_98 N N Streptococcus intermedius 1809 NR_028736 clade_98 N N Streptococcus lutetiensis 1810 NR_037096 clade_98 N N Streptococcus massiliensis 1811 AY769997 clade_98 N N Streptococcus mitis 1813 AM157420 clade_98 N N Streptococcus oligofermentans 1815 AY099095 clade_98 N N Streptococcus oralis 1816 ADMV01000001 clade_98 N N Streptococcus parasanguinis 1817 AEKM01000012 clade_98 N N Streptococcus pasteurianus 1818 AP012054 clade_98 N N Streptococcus peroris 1819 AEVF01000016 clade_98 N N Streptococcus pneumoniae 1820 AE008537 clade_98 N N Streptococcus porcinus 1821 EF121439 clade_98 N N Streptococcus pseudopneumoniae 1822 FJ827123 clade_98 N N Streptococcus pseudoporcinus 1823 AENS01000003 clade_98 N N Streptococcus pyogenes 1824 AE006496 clade_98 N OP Streptococcus ratti 1825 X58304 clade_98 N N Streptococcus salivarius 1826 AGBV01000001 clade_98 N N Streptococcus sanguinis 1827 NR_074974 clade_98 N N Streptococcus sinensis 1828 AF432857 clade_98 N N Streptococcus sp. 2_1_36FAA 1831 ACOI01000028 clade_98 N N Streptococcus sp. 2285_97 1830 AJ131965 clade_98 N N Streptococcus sp. ACS2 1834 HQ616360 clade_98 N N Streptococcus sp. AS20 1835 HQ616366 clade_98 N N Streptococcus sp. BS35a 1836 HQ616369 clade_98 N N Streptococcus sp. C150 1837 ACRI01000045 clade_98 N N Streptococcus sp. CM6 1838 HQ616372 clade_98 N N Streptococcus sp. ICM10 1840 HQ616389 clade_98 N N Streptococcus sp. ICM12 1841 HQ616390 clade_98 N N Streptococcus sp. ICM2 1842 HQ616386 clade_98 N N Streptococcus sp. ICM4 1844 HQ616387 clade_98 N N Streptococcus sp. ICM45 1843 HQ616394 clade_98 N N Streptococcus sp. M143 1845 ACRK01000025 clade_98 N N Streptococcus sp. M334 1846 ACRL01000052 clade_98 N N Streptococcus sp. oral clone ASB02 1849 AY923121 clade_98 N N Streptococcus sp. oral clone ASCA03 1850 DQ272504 clade_98 N N Streptococcus sp. oral clone ASCA04 1851 AY923116 clade_98 N N Streptococcus sp. oral clone ASCA09 1852 AY923119 clade_98 N N Streptococcus sp. oral clone ASCB04 1853 AY923123 clade_98 N N Streptococcus sp. oral clone ASCB06 1854 AY923124 clade_98 N N Streptococcus sp. oral clone ASCC04 1855 AY923127 clade_98 N N Streptococcus sp. oral clone ASCC05 1856 AY923128 clade_98 N N Streptococcus sp. oral clone ASCC12 1857 DQ272507 clade_98 N N Streptococcus sp. oral clone ASCD01 1858 AY923129 clade_98 N N Streptococcus sp. oral clone ASCD09 1859 AY923130 clade_98 N N Streptococcus sp. oral clone ASCD10 1860 DQ272509 clade_98 N N Streptococcus sp. oral clone ASCE03 1861 AY923134 clade_98 N N Streptococcus sp. oral clone ASCE04 1862 AY953253 clade_98 N N Streptococcus sp. oral clone ASCE05 1863 DQ272510 clade_98 N N Streptococcus sp. oral clone ASCE06 1864 AY923135 clade_98 N N Streptococcus sp. oral clone ASCE09 1865 AY923136 clade_98 N N Streptococcus sp. oral clone ASCE10 1866 AY923137 clade_98 N N Streptococcus sp. oral clone ASCE12 1867 AY923138 clade_98 N N Streptococcus sp. oral clone ASCF05 1868 AY923140 clade_98 N N Streptococcus sp. oral clone ASCF07 1869 AY953255 clade_98 N N Streptococcus sp. oral clone ASCF09 1870 AY923142 clade_98 N N Streptococcus sp. oral clone ASCG04 1871 AY923145 clade_98 N N Streptococcus sp. oral clone BW009 1872 AY005042 clade_98 N N Streptococcus sp. oral clone CH016 1873 AY005044 clade_98 N N Streptococcus sp. oral clone GK051 1874 AY349413 clade_98 N N Streptococcus sp. oral clone GM006 1875 AY349414 clade_98 N N Streptococcus sp. oral clone P2PA_41 P2 1876 AY207051 clade_98 N N Streptococcus sp. oral clone P4PA_30 P4 1877 AY207064 clade_98 N N Streptococcus sp. oral taxon 071 1878 AEEP01000019 clade_98 N N Streptococcus sp. oral taxon G59 1879 GU432132 clade_98 N N Streptococcus sp. oral taxon G62 1880 GU432146 clade_98 N N Streptococcus sp. oral taxon G63 1881 GU432150 clade_98 N N Streptococcus suis 1882 FM252032 clade_98 N N Streptococcus thermophilus 1883 CP000419 clade_98 N N Streptococcus uberis 1884 HQ391900 clade_98 N N Streptococcus urinalis 1885 DQ303194 clade_98 N N Streptococcus vestibularis 1886 AEKO01000008 clade_98 N N Streptococcus viridans 1887 AF076036 clade_98 N N Synergistetes bacterium oral clone 03 5 D05 1908 GU227192 clade_98 N N

List of Operational Taxonomic Units (OTU) with taxonomic assignments made to Genus, Species, and Phylogenetic Clade. Clade membership of bacterial OTUs is based on 16S sequence data. Clades are defined based on the topology of a phylogenetic tree that is constructed from full-length 16S sequences using maximum likelihood methods familiar to individuals with ordinary skill in the art of phylogenetics. Clades are constructed to ensure that all OTUs in a given clade are: (i) within a specified number of bootstrap supported nodes from one another, and (ii) within 5% genetic similarity. OTUs that are within the same clade can be distinguished as genetically and phylogenetically distinct from OTUs in a different clade based on 16S-V4 sequence data, while OTUs falling within the same clade are closely related. OTUs falling within the same clade are evolutionarily closely related and may or may not be distinguishable from one another using 16S-V4 sequence data. Members of the same clade, due to their evolutionary relatedness, play similar functional roles in a microbial ecology such as that found in the human gut. Compositions substituting one species with another from the same clade are likely to have conserved ecological function and therefore are useful in the present invention. All OTUs are denoted as to their putative capacity to form spores and whether they are a Pathogen or Pathobiont (see Definitions for description of “Pathobiont”). NIAID Priority Pathogens are denoted as ‘Category-A’, ‘Category-B’, or ‘Category-C’, and Opportunistic Pathogens are denoted as ‘OP’. OTUs that are not pathogenic or for which their ability to exist as a pathogen is unknown are denoted as ‘N’. The ‘SEQ ID Number’ denotes the identifier of the OTU in the Sequence Listing File and ‘Public DB Accession’ denotes the identifier of the OTU in a public sequence repository.

TABLE 2 L-glutamine nickel chloride BaCl₂ hemin potassium telurite Fibrinogen Bacto Vitamin-Free Casamino Acids cocarboxylase bovine albumin fraction V FeCl₂•H₂O L-cystine•2HCl Bacto Casamino Acids Agar CuSO₄ pyridoxine SnCl₂•2H₂O sodium selenite CaCl₂ NaCl albumin fraction V vitamin B₁₂ folic acid ZnCl₂ FeSO₄ oleic acid Co(NO₃)₂•6H₂O L-cystine Na₂B₄O₇•10H₂O CaSO₄•2H₂O AlCl₃ SeCl₄ Na₂MoO₄•2H₂O thiamine pyrophosphate Pyridoxine•HCI MnCl₂•4H₂O aluminum sulphate Na₂HPO₄ H₃BO₃ L-cysteine•HCl•H₂O adenine sulfate long-chain fatty acids KNO₃ sodium metabisulfite sodium molybdate CoCl₂•6H₂O Na₂MoO₄ Castenholz Salts NaNO₃ HCl L-cysteine copper sulfate L-cysteine•HCl thiamine•HCl biotin sodium chloride thallium acetate NiCl₂•6H₂O NaVO₃•H₂O nicotinamide adenine dinucleotide nicotinic acid Na₂MoO₄•H₂O CuCl₂•2H₂O FeCl₂•4H₂O (NH₄)₂MoO₄ MnSO₄ guanine•HCl H₂SO₄ CoCl₂ cholesterol LiCl pyridoxine•2HCI Disodium ethylenediamine tetraacetic acid Vitamin K1 KBr alkalinized oleic acid ZnSO₄•7H₂O trypsin inhibitor KI ethanol cobalt nitrate Ethylenediamine tetraacetic acid CuSO₄•5H₂O calcium-D-pathothenate Fe(NO₃)₃ CaCl₂•2H₂O Sodium pyruvate NaOH p-aminobenzoic acid a-ketoglutarate boric acid casein Pyridoxine hydrochloride Dried bovine hemoglobin ZnSO₄ Nicotinamide FeCl₃ Fe(NO₃)₃•6H₂O calcium pantothenate cyanocobalamin nitrilotriacetic acid Adenine sodium tartrate magnesium sulfate zinc sulfate NaHCO₃ Glucose MgSO₄•7H₂O Na₂S•9H₂O riboflavin ferric pyrophosphate Essential growth factors V and X Peptone FeSO₄•7H₂O catalase MnSO₄•7H₂O CuCl₂ Na₂SeO₃•5H₂O thiamine NiCl₂ sodium tungstate iron sulfate calcium chloride (NH₄)₆Mo₇O₂₄•4H₂O ACES buffer/KOH Thioctic acid succinate formate lactate butyrate acetate Vitamin K Mercaptoethane-sulfonic acid Lipoic acid ammonia heme S-Adenosylmethionine

Representative Vitamins, Minerals, and Cofactors

TABLE 3 Phylogenetic Spore Forming Dominant OTU in OTU Clade OTU Augmented Ecology Bacteroides sp. 2_1_22 clade38 N Y Streptococcus anginosus clade60 N Prevotella intermedia clade81 N Prevotella nigrescens clade81 N Oribacterium sp. ACB7 clade90 N Prevotella salivae clade104 N Bacteroides intestinalis clade171 N Y Bifidobacterium dentium clade172 N Alcaligenes faecalis clade183 N Rothia dentocariosa clade194 N Peptoniphilus lacrimalis clade291 N Anaerococcus sp. gpac155 clade294 N Sutterella stercoricanis clade302 N Y Bacteroides sp. 3_1_19 clade335 N Y Parabacteroides goldsteinii clade335 N Bacteroides dorei clade378 N Y Bacteroides massiliensis clade378 N Lactobacillus iners clade398 N Granulicatella adiacens clade460 N Eggerthella sp. 1_3_56FAA clade477 N Gordonibacter pamelacae clade477 N Finegoldia magna clade509 N Actinomyces nasicola clade523 N Streptobacillus moniliformis clade532 N Oscillospira guilliermondii clade540 N Orientia tsutsugamushi clade541 N Christensenella minuta clade558 N Clostridium oroticum clade96 Y Clostridium sp. D5 clade96 Y Clostridium glycyrrhizinilyticum clade147 Y Coprococcus comes clade147 Y Ruminococcus lactaris clade147 Y Ruminococcus torques clade147 Y Y Clostridiales sp. SS3/4 clade246 Y Clostridium hylemonae clade260 Y Clostridium aerotolerans clade269 Y Clostridium asparagiforme clade300 Y Y Clostridium sp. M62/1 clade300 Y Clostridium symbiosum clade300 Y Lachnospiraceae genomosp. C1 clade300 Y Blautia sp. M25 clade304 Y Y Blautia stercoris clade304 Y Ruminococcus hansenii clade304 Y Ruminococcus obeum clade304 Y Ruminococcus sp. 5_1_39BFAA clade304 Y Bryantella formatexigens clade309 Y Eubacterium cellulosolvens clade309 Y Clostridium sp. HGF2 clade351 Y Clostridium bartlettii clade354 Y Clostridium bifermentans clade354 Y Clostridium glycolicum clade354 Y Eubacterium tenue clade354 Y Dorea formicigenerans clade360 Y Dorea longicatena clade360 Y Lachnospiraceae bacterium 2_1_46FAA clade360 Y Lachnospiraceae bacterium 9_1_43BFAA clade360 Y Y Ruminococcus gnavus clade360 Y Clostridium hathewayi clade362 Y Blautia hydrogenotrophica clade368 Y Clostridiaceae bacterium END-2 clade368 Y Roseburia faecis clade369 Y Roseburia hominis clade370 Y Roseburia intestinalis clade370 Y Eubacterium sp. WAL 14571 clade384 Y Erysipelotrichaceae bacterium 5_2_54FAA clade385 Y Eubacterium biforme clade385 Y Eubacterium dolichum clade385 Y Coprococcus catus clade393 Y Acetivibrio ethanolgignens clade396 Y Anaerosporobacter mobilis clade396 Y Bacteroides pectinophilus clade396 Y Eubacterium hallii clade396 Y Eubacterium xylanophilum clade396 Y Anaerostipes caccae clade408 Y Clostridiales bacterium 1_7_47FAA clade408 Y Clostridium aldenense clade408 Y Clostridium citroniae clade408 Y Eubacterium hadrum clade408 Y Y Acetanaerobacterium elongatum clade439 Y Faecalibacterium prausnitzii clade478 Y Gemmiger formicilis clade478 Y Y Eubacterium ramulus clade482 Y Lachnospiraceae bacterium 3_1_57FAA_CT1 clade483 Y Lachnospiraceae bacterium A4 clade483 Y Y Lachnospiraceae bacterium DJF VP30 clade483 Y Holdemania filiformis clade485 Y Clostridium orbiscindens clade494 Y Pseudoflavonifractor capillosus clade494 Y Ruminococcaceae bacterium D16 clade494 Y Acetivibrio cellulolyticus clade495 Y Eubacterium limosum clade512 Y Anaerotruncus colihominis clade516 Y Clostridium methylpentosum clade516 Y Clostridium sp. YIT 12070 clade516 Y Hydrogenoanaerobacterium saccharovorans clade516 Y Eubacterium ventriosum clade519 Y Eubacterium eligens clade522 Y Lachnospira pectinoschiza clade522 Y Lactobacillus rogosae clade522 Y Y Clostridium leptum clade537 Y Eubacterium coprostanoligenes clade537 Y Ruminococcus bromii clade537 Y Clostridium viride clade540 Y Butyrivibrio crossotus clade543 Y Coprococcus eutactus clade543 Y Eubacterium ruminantium clade543 Y Eubacterium rectale clade568 Y Y Roseburia inulinivorans clade568 Y Butyricicoccus pullicaecorum clade572 Y Eubacterium desmolans clade572 Y Papillibacter cinnamivorans clade572 Y Sporobacter termitidis clade572 Y Clostridium lactatifermentans clade576 Y

Bacterial OTUs associated with engraftment and ecological augmentation and establishment of a more diverse microbial ecology in patients treated with an ethanol-treated spore preparation. OTUs that comprise an augmented ecology are not present in the patient prior to treatment and/or exist at extremely low frequencies such that they do not comprise a significant fraction of the total microbial carriage and are not detectable by genomic and/or microbiological assay methods. OTUs that are members of the engrafting and augmented ecologies were identified by characterizing the OTUs that increase in their relative abundance post treatment and that respectively are: (i) present in the ethanol-treated spore preparation and absent in the patient pretreatment, or (ii) absent in the ethanol-treated spore preparation, but increase in their relative abundance through time post treatment with the preparation due to the formation of favorable growth conditions by the treatment. Notably, the latter OTUs can grow from low frequency reservoirs in the patient, or be introduced from exogenous sources such as diet. OTUs that comprise a “core” augmented or engrafted ecology can be defined by the percentage of total patients in which they are observed to engraft and/or augment; the greater this percentage the more likely they are to be part of a core ecology responsible for catalyzing a shift away from a dysbiotic ecology. The dominant OTUs in an ecology can be identified using several methods including but not limited to defining the OTUs that have the greatest relative abundance in either the augmented or engrafted ecologies and defining a total relative abundance threshold. As example, the dominant OTUs in the augmented ecology of Patient-1 were identified by defining the OTUs with the greatest relative abundance, which together comprise 60% of the microbial carriage in this patient's augmented ecology.

TABLE 4 Pretreatment Day 5 Day 14 Day 25 Klebsiella (% of total reads) 20.27% 1.32% 7.62% 0.00% Fusobacterium (% total of reads) 19.14% 3.01% 0.01% 0.00%

Reduction in pathogen carriage post treatment with bacterial composition treatment of Patient 1.

TABLE 5 Media Bacteroides species Pretreatment titer (cfu/g) Day 25 titer (cfu/g) BBE B. fragilis group <2 × 10⁴ 3 × 10⁸ PFA All Bacteroides <2 × 10⁷ 2 × 10¹⁰

Augmentation of Bacteroides as a function of bacterial composition treatment of Patient 1.

TABLE 6 % of Spore % of Patients Preps with OTU Spore Keystone OTU Clade OTU Engrafts Former OTU Prevotella_maculosa clade_104  10%  0% N N Prevotella_copri clade_168  20%  0% N N Bacteroides_caccae clade_170  30%  0% N Y Bifidobacterium_sp_TM_7* clade_172  90% 60% N N Bifidobacterium_gallicum clade_172  70% 20% N N Bifidobacterium_dentium clade_172  50%  0% N N Lactobacillus_casei clade_198  20% 10% N N Actinomyces_odontolyticus clade_212  20% 30% N N Clostridium_colicanis clade_223  10% 10% Y N Clostridiales_sp_SS3_4* clade_246 100% 70% Y N Clostridium_sporogenes clade_252  40% 40% Y N Clostridium_butyricum clade_252  20% 20% Y N Clostridium_disporicum clade_253  40% 30% Y N Clostridium_hylemonae* clade_260 100% 50% Y N Clostridium_scindens clade_260  10% 60% Y N Coprococcus_comes* clade_262  90% 80% Y Y Lachnospiraceae_bacterium_1_4_56FAA* clade_262  90% 80% Y Y Ruminococcus_torques clade_262  30% 70% Y Y Parabacteroides_merdae clade_286  30% 20% N Y Bifidobacterium_bifidum clade_293  10%  0% N N Johnsonella_ignava clade_298  10% 10% N N Blautia_glucerasea* clade_309 100% 80% Y N Blautia_sp_M25* clade_309 100% 70% Y Y Lachnospiraceae_bacterium_6_1_63FAA* clade_309 100% 60% Y N Eubacterium_cellulosolvens clade_309  10% 30% Y Y Lactobacillus_fermentum clade_313  10%  0% N N Sarcina_ventriculi clade_353  10% 10% Y N Clostridium_bartlettii* clade_354  90% 70% Y N Clostridium_bifermentans clade_354  70% 70% Y N Clostridium_mayombei clade_354  50% 50% Y N Dorea_longicatena* clade_360 100% 60% Y Y Lachnospiraceae_bacterium_9_1_43BFAA clade_360 100% 30% Y N Lachnospiraceae_bacterium_2_1_58FAA* clade_360  80% 80% Y N Lachnospiraceae_bacterium_2_1_46FAA clade_360  50% 50% Y N Lactobacillus_perolens clade_373  10%  0% N N Bacteroides_dorei clade_378  60% 50% N Y Eubacterium_biforme clade_385  10%  0% Y N Peptoniphilus_sp_gpac077 clade_389  10% 20% N N Coprococcus_catus* clade_393 100% 70% Y Y Eubacterium_hallii* clade_396  90% 60% Y Y Anaerosporobacter_mobilis clade_396  40% 60% Y N Bacteroides_pectinophilus clade_396  10% 60% Y N Lactobacillus_hominis clade_398  10%  0% N N Lactococcus_lactis clade_401  40% 40% N N Ruminococcus_champanellensis* clade_406  80% 50% Y N Ruminococcus_callidus clade_406  10% 10% Y N Clostridium_clostridioforme* clade_408 100% 60% Y Y Eubacterium_hadrum* clade_408 100% 90% Y Y Clostridium_symbiosum clade_408  30% 50% Y Y Anaerostipes_caccae clade_408  10% 50% Y N Parasutterella_excrementihominis clade_432  10%  0% N N Sutterella_sterconcanis clade_432  10%  0% N N Eubacterium_rectale* clade_444 100% 80% Y Y Lachnobacterium_bovis* clade_444 100% 80% Y N Desulfovibrio_desulfuncans clade_445  10%  0% N Y Eubacterium_sp_oral_clone_JS001* clade_476  80% 70% Y N Faecalibacterium_prausnitzii* clade_478 100% 60% Y Y Subdoligranulum_variabile* clade_478 100% 80% Y Y Coprobacillus_sp_D7* clade_481  90% 60% Y N Clostridium_cocleatum clade_481  60% 20% Y N Clostridium_spiroforme clade_481  40% 50% Y N Eubacterium_ramulus* clade_482  80% 60% Y N Flavonifractor_plautii clade_494  70% 60% Y Y Pseudoflavonifractor_capillosus clade_494  60% 60% Y Y Ruminococcaceae_bacterium_D16 clade_494  30% 50% Y Y Acetivibrio_cellulolyticus* clade_495  70% 80% Y N Clostridium_stercorarium clade_495  40% 50% Y N Enterococcus_durans clade_497  10% 10% N N Enterococcus_faecium clade_497  10% 10% N N Dialister_invisus clade_506  50% 10% N N Eubacterium_limosum clade_512  20%  0% Y N Ruminococcus_flavefaciens clade_516  60% 60% Y N Eubacterium_ventriosum clade_519  30% 60% Y Y Bilophila_wadsworthia clade_521  90%  0% N Y Lachnospira_pectinoschiza clade_522  40% 60% Y N Eubacterium_eligens clade_522  30% 50% Y Y Catonella_morbi clade_534  20%  0% N N Clostridium_sporosphaeroides* clade_537 100% 80% Y N Ruminococcus_bromii clade_537  60% 30% Y Y Clostridium_leptum clade_537  40% 70% Y Y Clostridium_sp_YIT_12069 clade_537  40% 60% Y N Clostridium_viride clade_540  10% 10% Y N Megamonas_funiformis clade_542  50%  0% N N Eubacterium_ruminantium* clade_543  80% 90% Y N Coprococcus_eutactus clade_543  20% 20% Y N Collinsella_aerofaciens clade_553  50% 10% Y Y Alkaliphilus_metalliredigenes clade_554  40% 10% Y N Turicibacter_sanguinis clade_555  80% 40% Y N Phascolarctobacterium_faecium clade_556  20%  0% N N Clostridiales_bacterium_oral_clone_P4PA* clade_558  80% 50% N N Lutispora_thermophila clade_564 100%  0% Y N Coriobacteriaceae_bacterium_JC110 clade_566  70%  0% N N Eggerthella_sp_1_3_56FAA clade_566  70% 30% N N Adlercreutzia_equolifaciens clade_566  40%  0% N N Gordonibacter_pamelaeae clade_566  30%  0% N Y Slackia_isoflavoniconvertens clade_566  10%  0% N N Eubacterium_desmolans* clade_572  90% 70% Y N Papillibacter_cinnamivorans* clade_572  90% 80% Y N Clostridium_colinum clade_576  30% 30% Y N Akkermansia_muciniphila clade_583  60% 10% N Y Clostridiales_bacterium_oral_taxon_F32 clade_584  60% 30% N N Prochlorococcus_marinus clade_592  30%  0% N N Methanobrevibacter_wolinii clade_595  30%  0% N N Bacteroides_fragilis clade_65  20% 30% N Y Lactobacillus_delbrueckii clade_72  10%  0% N N Escherichia_coli clade_92  50%  0% N Y Clostridium_sp_D5 clade_96  80% 60% Y N Streptococcus_thermophilus clade_98  90% 20% N Y Streptococcus_sp_CM6 clade_98  20% 10% N N Streptococcus_sp_oral_clone_ASCE05 clade_98  10%  0% N N

OTUs detected by a minimum of ten 16S-V4 sequence reads in at least a one ethanol-treated spore preparation. OTUs that engraft in a treated patients and the percentage of patients in which they engraft are denoted, as are the clades, spore forming status, and Keystone OTU status. Starred OTUs occur in ≥80% of the ethanol preps and engraft in ≥50% of the treated patients.

TABLE 7 OTU Clade CES Spore Former Keystone OTU Eubacterium_hadrum clade_408 4.2 Y Y Eubacterium_rectale clade_444 4.2 Y Y Subdoligranulum_variabile clade_478 4.2 Y Y Blautia_sp_M25 clade_309 4.2 Y Y Coprococcus_catus clade_393 4.2 Y Y Lachnospiraceae_bacterium_1_4_56FAA clade_262 4.2 Y Y Coprococcus_comes clade_262 4.2 Y Y Blautia_glucerasea clade_309 4.0 Y N Lachnobacterium_bovis clade_444 4.0 Y N Clostridium_sporosphaeroides clade_537 4.0 Y N Clostridiales_sp_SS3_4 clade_246 4.0 Y N Papillibacter_cinnamivorans clade_572 4.0 Y N Clostridium_bartlettii clade_354 4.0 Y N Eubacterium_desmolans clade_572 4.0 Y N Clostridium_clostridioforme clade_408 3.2 Y Y Dorea_longicatena clade_360 3.2 Y Y Faecalibacterium_prausnitzii clade_478 3.2 Y Y Eubacterium_hallii clade_396 3.2 Y Y Clostridium_leptum clade_537 3.2 Y Y Lachnospiraceae_bacterium_6_1_63FAA clade_309 3.0 Y N

Top 20 OTUs Ranked by CES

Lengthy table referenced here US20180353554A1-20181213-T00001 Please refer to the end of the specification for access instructions.

TABLE 9 Disease Indication for which Health Keystone OTU Clade Family Genus OTU Akkermansia muciniphila clade_583 Verrucomicrobiaceae Akkermansia CDAD Alistipes putredinis clade_500 Rikenellaceae Alistipes CDAD, T2D Alistipes shahii clade_500 Rikenellaceae Alistipes CDAD, T2D Bacteroides caccae clade_170 Bacteroidaceae Bacteroides CDAD, Obesity Bacteroides cellulosilyticus clade_85 Bacteroidaceae Bacteroides CDAD, T2D Bacteroides dorei clade_378 Bacteroidaceae Bacteroides CDAD, Obesity, T2D Bacteroides eggerthii clade_85 Bacteroidaceae Bacteroides T2D Bacteroides finegoldii clade_170 Bacteroidaceae Bacteroides CDAD, UC Bacteroides intestinalis clade_171 Bacteroidaceae Bacteroides T2D Bacteroides ovatus clade_38 Bacteroidaceae Bacteroides Obesity, T2D Bacteroides sp. D20 clade_110 Bacteroidaceae Bacteroides CDAD CDAD, T2D, Bacteroides stercoris clade_85 Bacteroidaceae Bacteroides UC Bacteroides thetaiotaomicron clade_65 Bacteroidaceae Bacteroides CDAD, Obesity Bacteroides uniformis clade_110 Bacteroidaceae Bacteroides T2D, UC Bacteroides xylanisolvens clade_38 Bacteroidaceae Bacteroides Obesity Bifidobacterium longum clade_172 Bifidobacteriaceae Bifidobacterium CDAD Bilophila wadsworthia clade_521 Desulfovibrionaceae Bilophila CDAD Blautia sp. M25 clade_309 Lachnospiraceae Blautia CDAD Butyricicoccus pullicaecorum clade_572 Clostridiaceae Butyricicoccus CDAD Butyrivibrio crossotus clade_543 Lachnospiraceae Butyrivibrio CDAD Catenibacterium mitsuokai clade_469 Erysipelotrichaceae Catenibacterium Obesity Clostridium lactatifermentans clade_576 Clostridiaceae Clostridium CDAD Clostridium leptum clade_537 Clostridiaceae Clostridium CDAD, Obesity, T2D Clostridium nexile clade_262 Clostridiaceae Clostridium CDAD Clostridium sp. NML 04A032 clade_494 Clostridiaceae Clostridium CDAD Coprococcus catus clade_393 Lachnospiraceae Coprococcus CDAD, T2D Coprococcus comes clade_262 Lachnospiraceae Coprococcus CDAD, T2D Desulfovibrio desulfuricans clade_445 Desulfovibrionaceae Desulfovibrio T2D Desulfovibrio piger clade_445 Desulfovibrionaceae Desulfovibrio Obesity Dorea formicigenerans clade_360 Lachnospiraceae Dorea CDAD, T2D Dorea longicatena clade_360 Lachnospiraceae Dorea CDAD, T2D Eubacterium coprostanoligenes clade_537 Eubacteriaceae Eubacterium CDAD Eubacterium eligens clade_522 Eubacteriaceae Eubacterium T2D Eubacterium hadrum clade_408 Lachnospiraceae Anaerostipes CDAD Eubacterium hallii clade_396 Eubacteriaceae Eubacterium CDAD, T2D Eubacterium rectale clade_444 Eubacteriaceae Eubacterium CDAD, T2D Eubacterium siraeum clade_538 Eubacteriaceae Eubacterium CDAD Eubacterium ventriosum clade_519 Eubacteriaceae Eubacterium T2D Faecalibacterium prausnitzii clade_478 Ruminococcaceae Faecalibacterium CDAD, T2D Gemmiger formicilis clade_478 Hyphomicrobiaceae Gemmiger CDAD Gordonibacter pamelaeae clade_566 Coriobacteriaceae Gordonibacter Obesity Holdemania filiformis clade_485 Erysipelotrichaceae Holdemania CDAD, Obesity, T2D Lachnospiraceae bacterium 1_4_56FAA clade_262 Lachnospiraceae CDAD Lachnospiraceae bacterium 3_1_57FAA_CT1 clade_408 Lachnospiraceae CDAD Odoribacter splanchnicus clade_466 Porphyromonadaceae Odoribacter CDAD, T2D Oscillibacter valericigenes clade_540 Oscillospiraceae Oscillibacter CDAD Oxalobacter formigenes clade_357 Oxalobacteraceae Oxalobacter T2D Parabacteroides johnsonii clade_286 Porphyromonadaceae Parabacteroides CDAD, T2D Parabacteroides merdae clade_286 Porphyromonadaceae Parabacteroides CDAD, Obesity, T2D Pseudoflavonifractor capillosus clade_494 Pseudoflavonifractor T2D Roseburia hominis clade_444 Lachnospiraceae Roseburia CDAD Roseburia intestinalis clade_444 Lachnospiraceae Roseburia CDAD, T2D Roseburia inulinivorans clade_444 Lachnospiraceae Roseburia CDAD, T2D Ruminococcus bromii clade_537 Ruminococcaceae Ruminococcus CDAD Ruminococcus lactaris clade_262 Ruminococcaceae Ruminococcus CDAD Ruminococcus obeum clade_309 Lachnospiraceae Blautia CDAD, T2D Ruminococcus torques clade_262 Lachnospiraceae Blautia CDAD, T2D Sporobacter termitidis clade_572 Ruminococcaceae Sporobacter CDAD Streptococcus parasanguinis clade_98 Streptococcaceae Streptococcus CDAD Subdoligranulum variabile clade_478 Ruminococcaceae Subdoligranulum CDAD Veillonella atypica clade_358 Veillonellaceae Veillonella CDAD Veillonella parvula clade_358 Veillonellaceae Veillonella CDAD Victivallis vadensis clade_567 Victivallaceae Victivallis UC

Keystone OTUs that occur in Network Ecologies representing states of health for various disease indications (CDAD=Clostridium difficile associated diarrhea, T2D=Type 2 Diabetes, Obesity=clinical obesity, UC=ulcerative colitis)

TABLE 10 Non-Keystone OTUs Acidaminococcus fermentans Acinetobacter johnsonii Alistipes indistinctus Anaerostipes caccae Anaerotruncus colihominis Auritibacter ignavus Bacteroides coprocola Bacteroides coprophilus Bacteroides fragilis Bacteroides pectinophilus Bacteroides plebeius Bacteroides salanitronis Bacteroides sp. 1_1_30 Bacteroides sp. 20_3 Bacteroides sp. 3_1_40A Bacteroides sp. D2 Bacteroides vulgatus Barnesiella viscericola Bifidobacterium adolescentis Bifidobacterium bifidum Bifidobacterium catenulatum Bifidobacterium dentium Bifidobacterium pseudocatenulatum Blautia hansenii Blautia hydrogenotrophica Blautia producta Campylobacter hominis Campylobacter upsaliensis Capnocytophaga sp. oral clone ASCH05 Capnocytophaga sp. oral taxon 338 Chlamydiales bacterium NS13 Chromobacterium violaceum Citrobacter sp. 30_2 Clostridiales bacterium oral clone P4PA Clostridiales sp. SS3/4 Clostridium asparagiforme Clostridium bartlettii Non-Keystone OTUs Clostridium beijerinckii Clostridium bifermentans Clostridium bolteae Clostridium botulinum Clostridium butyricum Clostridium celatum Clostridium cocleatum Clostridium glycolicum Clostridium hathewayi Clostridium hylemonae Clostridium innocuum Clostridium methylpentosum Clostridium orbiscindens Clostridium ramosum Clostridium scindens Clostridium symbiosum Clostridium tertium Clostridium thermocellum Collinsella aerofaciens Collinsella tanakaei Coprobacillus sp. D7 Coprococcus eutactus Corynebacterium pseudogenitalium Dialister invisus Eggerthella lenta Enhydrobacter aerosaccus Enterococcus raffinosus Enterococcus sp. CCRI 16620 Escherichia coli Eubacterium desmolans Eubacterium nodatum Eubacterium sp. WAL 14571 Eubacterium tenue Gardnerella vaginalis Granulicatella adiacens Haemophilus parainfluenzae Halorubrum lipolyticum Heliobacterium modesticaldum Lachnobacterium bovis Lachnospiraceae bacterium 1_1_57FAA Non-Keystone OTUs Lachnospiraceae bacterium 5_1_57FAA Lactobacillus ruminis Lactococcus lactis Marvinbryantia formatexigens Methanobrevibacter smithii Mitsuokella multacida Mycoplasmataceae genomosp P1 oral clone Neisseria meningitidis Parabacteroides distasonis Peptoniphilus sp. gpac077 Phascolarctobacterium sp. YIT 12068 Porphyromonas asaccharolytica Prevotella buccae Prevotella buccalis Prevotella copri Propionibacterium acnes Proteus penneri Psychrobacter pulmonis Roseburia faecalis Rothia mucilaginosa Ruminococcus albus Ruminococcus gnavus Ruminococcus sp. ID8 Scardovia inopinata Solobacterium moorei Staphylococcus warneri Streptococcus australis Streptococcus dysgalactiae Streptococcus infantis Streptococcus mitis Streptococcus peroris Streptococcus pyogenes Streptococcus salivarius Streptococcus sanguinis Streptococcus sp. oral clone ASCF07 Streptococcus suis Streptococcus thermophilus Streptococcus vestibularis Sutterella wadsworthensis Synergistetes bacterium oral taxon D48 Non-Keystone OTUs Tannerella sp. 6_1_58FAA_CT1 Tissierella praeacuta Veillonella dispar

Non-Keystone OTUs that Occur in Network Ecologies Representing States of Health

TABLE 11 Network Ecology ID Eubacterium_eligens Roseburia_intestinalis Ruminococcus_gnavus Clostridium_symbiosum (a) N1 X X X X N2 X X X X N3 X X X X N4 X X X X N5 X X X X N6 X X X X N7 X X X X N8 X X X X N9 X X X X N10 X X X X N11 X X X X N12 X X X N13 X X X N14 X X X N15 X X X N16 X X X N17 X X X N18 X X X N19 X X X N20 X X X N21 X X X N22 X X X N23 X X X N24 X X X N25 X X X N26 X X X N27 X X X N28 X X X N29 X X X N30 X X X N31 X X X N32 X X X N33 X X X N34 X X X N35 X X X N36 X X X N37 X X X N38 X X X (b) N39 X X X N40 X X X N41 X X X N42 X X N43 X X N44 X X N45 X X N46 X X N47 X X N48 X X N49 X X N50 X X N51 X X N52 X X N53 X X N54 X X N55 X X N56 X X N57 X X N58 X X X N59 X X X N60 X X X N61 X X X N62 X X X N63 X X X N64 X X X N65 X X X N66 X X X N67 X X X N68 X X X N69 X X X N70 X X X N71 X X X N72 X X X N73 X X N74 X X N75 X X N76 X X (c) N77 X X N78 X X N79 X X N80 X X N81 X X N82 X X N83 X X N84 X X N85 X X N86 X X N87 X X N88 X X N89 X X N90 X X N91 X X N92 X X N93 X X N94 X X N95 X X N96 X X N97 X X N98 X X N99 X X N100 X X N101 X X N102 X X N103 X X N104 X X N105 X N106 X N107 X N108 X N109 X N110 X N111 X N112 X N113 X N114 X (d) N115 X N116 X N117 X N118 X N119 X N120 X X X N121 X X X N122 X X X N123 X X X N124 X X X N125 X X X N126 X X X N127 X X X N128 X X X N129 X X X N130 X X X N131 X X X N132 X X X N133 X X X N134 X X X N135 X X N136 X X N137 X X N138 X X N139 X X N140 X X N141 X X N142 X X N143 X X N144 X X N145 X X N146 X X N147 X X N148 X X N149 X X N150 X X N151 X X N152 X X (e) N153 X X N154 X X N155 X X N156 X X N157 X X N158 X X NI59 X X N160 X X N161 X X N162 X X N163 X X N164 X X N165 X X N166 X X N167 X N168 X N169 X N170 X N171 X N172 X N173 X N174 X N175 X N176 X N177 X N178 X N179 X N180 X N181 X N182 X X N183 X X N184 X X N185 X X N186 X X N187 X X N188 X X N189 X X N190 X X (f) N191 X X N192 X X N193 X X N194 X X N195 X X N196 X X N197 X X N198 X N199 X N200 X N201 X N202 X N203 X N204 X N205 X N206 X N207 X N208 X N209 X N210 X N211 X N212 X N213 X N214 X N215 X N216 X N217 X M218 X N219 X N220 N221 N222 N223 Network Ecology ID Coprococcus_comes Dorea_longicatena Subdoligranulum_variabile Faecalibacterium_prausnitzii (a) N1 X X N2 X X N3 X X N4 X N5 X X N6 X X N7 X N8 X X N9 X N10 X N11 N12 X X X N13 X X X N14 X X N15 X X X N16 X X N17 X X N18 X N19 X X X N20 X X N21 X X N22 X N23 X X N24 X N25 X N26 N27 X X X N28 X X X N29 X X N30 X X X N31 X X N32 X X N33 X N34 X X X N35 X X N36 X X N37 X N38 X X (b) N39 X N40 X N41 N42 X X X X N43 X X X N44 X X X N45 X X N46 X X X N47 X X N48 X X N49 X N50 X X X N51 X X N52 X X N53 X N54 X X N55 X N56 X N57 N58 X X X N59 X X X N60 X X N61 X X X N62 X X N63 X X N64 X N65 X X X N66 X X N67 X X N68 X N69 X X N70 X N71 X N72 N73 X X X X N74 X X X N75 X X X N76 X X (c) N77 X X X N78 X X N79 X X N80 X N81 X X X N82 X X N83 X X N84 X N85 X X N86 X N87 X N88 N89 X X X X N90 X X X N91 X X X N92 X X N93 X X X N94 X X N95 X X N96 X N97 X X X N98 X X N99 X X N100 X N101 X X N102 X N103 X N104 N105 X X X X N106 X X X N107 X X X N108 X X N109 X X X N110 X X N111 X X N112 X N113 X X X N114 X X (d) N115 X X N116 X N117 X X N118 X N119 X N120 X X X N121 X X X N122 X X N123 X X X N124 X X N125 X X N126 X N127 X X X N128 X X N129 X X N130 X N131 X X N132 X N133 X N134 N135 X X X X N136 X X X N137 X X X N138 X X N139 X X X N140 X X N141 X X N142 X N143 X X X N144 X X N145 X X N146 X N147 X X N148 X N149 X N150 N151 X X X X N152 X X X (e) N153 X X X N154 X X N155 X X X N156 X X N157 X X N158 X N159 X X X N160 X X N161 X X N162 X N163 X X N164 X N165 X N166 N167 X X X X N168 X X X N169 X X X N170 X X N171 X X X N172 X X N173 X X N174 X N175 X X X N176 X X N177 X X N178 X N179 X X N180 X N181 X N182 X X X X N183 X X X N184 X X X N185 X X N186 X X X N187 X X N188 X X N189 X N190 X X X (f) N191 X X N192 X X N193 X N194 X X N195 X N196 X N197 N198 X X X X N199 X X X N200 X X X N201 X X N202 X X X N203 X X N204 X X N205 X N206 X X X N207 X X N208 X X N209 X N210 X X N211 X N212 X N213 X X X N214 X X N215 X X N216 X N217 X X M218 X N219 X N220 X X X N221 X X N222 X X N223 X X

Exemplary Functional Network Ecologies that are found only in healthy individuals, that contain only Keystone OTUs, and that have OTUs with the functional capacity to form spores.

TABLE 12 (a) Core Network ID Faecalibacterium_prausnitzii Ruminococcus_obeum Alistipes_putredinis Alistipes_shahii Ruminococcus_torques Coprococcus_catus Dorea_longicatena Core 1 100 100 15 15 99 99 100 Core 2 100 100 100 100 14 100 100 Core 3 100 100 100 100 8 5 100 Core 4 100 100 100 100 100 11 11 Core 5 100 100 100 100 100 97 20 Core 6 100 100 100 100 100 100 11 Core Network ID Eubacterium_rectale Bifidobacterium_adaolescentis Coprococcus_comes Roseburia_inulinivorans Clostridium_leptum Cordonibacter_pamelaeae Core 1 100 9 13 99 13 Core 2 100 100 1 14 16 Core 3 100 100 100 8 8 Core 4 14 94 10 98 98 Core 5 17 7 13 91 99 Core 6 11 2 82 100 10 19 (b) Core Network ID Dorea_formicigenerans Eubacterium_eligens Eubacterium_hallii Subdoligranulum_variabile Bacteroides_ovatus Core 1 13 12 11 13 11 Core 2 16 15 14 16 10 Core 3 8 8 8 8 8 Core 4 13 11 11 11 11 Core 5 19 20 19 12 17 Core 6 11 9 10 9 9 Core Network ID Eubacterium_ventrisum Anaerotruncus_colihominis Bacteroides_vulgatus Bacteroides_xylanisolvens Roseburia_intestinalis Core 1 12 9 9 9 11 Core 2 14 10 11 19 9 Core 3 8 8 7 8 8 Core 4 10 10 15 7 6 Core 5 13 16 7 7 Core 6 9 10 10 5 5 (c) Core Network ID Bacteroides_uniformis Holdemania_filiformis Parabacteroides_merdae Collinsella_aerofaciens Bacteroides_dorei Odoribacter_splanchnicus Core 1 7 7 6 7 8 Core 2 7 3 8 6 7 Core 3 7 7 7 7 7 7 Core 4 5 6 6 5 3 7 Core 5 6 10 4 Core 6 4 4 3 4 3 6 Core Network ID Bilophilia_wadsworthia Ruminococcus_lactaris Bacteroides_finegoldii Bacteroides_thetaiotaomicron Ruminococcus_gnavus Bacteroides_caccae Core 1 3 Core 2 Core 3 6 7 6 6 4 6 Core 4 5 7 5 4 5 1 Core 5 4 Core 6 4 3 6 6 3 4 Core Network ID Bacteroides_stercoris Akkermansia_muciniphila Bifidobacterium_longum Eubacterium_siraeum Ruminococcus_bromii Bacteroides_cellulosilyticus Core 1 Core 2 Core 3 4 5 4 2 2 Core 4 1 Core 5 Core 6 3 3 3 3 3 3

Exemplary Network Ecologies Classes (a.k.a Core) defined from their occurrence in only healthy individuals, the size of the network, and the frequency of occurrence of the networks in individual subjects at or above the 90^(th) percentile for the latter two metrics. OTUs represent diverse taxonomic families (see Table 1). Numbers in each cell represent the percentage of individual observed Network Ecologies within a given Network Class that contain the given OTU. (a) OTUs that are observed in at least 80% of a core's networks are primary signature OTUs of a given core. (b-c) OTUs observed in 11%-79% and <10% are secondary and tertiary signature OTUs respectively of a given Network Class. Primary signature OTUs are of greater significance than secondary signature OTUs which are of greater significance than tertiary keystone OTUs.

TABLE 13 Core Network ID Ruminococcaceae** Rikenellaceae Lachnospiraceae** Eubacteriaceae* bifidobacteriaceae Clostridiaceae* Coriobacteriaceae Core 1 X X X X Core 2 X X X X X Core 3 X X X X X Core 4 X X X X X Core 5 X X X X X Core 6 X X X

Network Ecologies Classes (a.k.a. Core) encompass specific phylogenetic signature families based on inclusion of OTUs that are observed in at least 80% of a Class' networks.

TABLE 14A Per- Per- cent of Num. Num. cent of Key- of of OTUs stone Clades OTUs that OTUs Net- in Net- in Net- are in Net- work work work Spore work Ecol-ogy Ecol- Ecol- Form- Ecol- Exemplary Network Exemplary Network Exemplary Keystone ID ogy ogy ers ogy clades OTUs OTUs N262.S 10 15 80 93.3 (clade_172 or Alistipes putredinis, Alistipes putredinis, clade_172i), (clade_262 Bifidobacterium dentium, Bifidobacterium longum, or clade_262i), Bifidobacterium longum, Coprococcus comes, (clade_360 or clade_360c Coprococcus comes, Dorea Dorea longicatena, or clade_360g or longicatena, Eubacterium Eubacterium eligens, clade_360h or eligens, Eubacterium hallii, Eubacterium hallii, clade_360i), clade_396, Eubacterium rectale, Eubacterium rectale, (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Holdemania prausnitzii, Holdemania or clade_478i), filiformis, filiformis, clade_485, clade_494, Pseudoflavonifractor Pseudoflavonifractor clade_500, (clade_522 or capillosus, Roseburia capillosus, Roseburia clade_522i) intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N290.S 10 14 92.9 92.9 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus catus, Coprococcus catus, or clade_360c or Coprococcus comes, Coprococcus comes, clade_360g or clade_360h Coprococcus eutactus, Dorea longicatena, or clade_360i), Dorea longicatena, Eubacterium eligens, clade_393, clade_396, Eubacterium eligens, Eubacterium hallii, (clade_444 or Eubacterium hallii, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, clade_494, clade_500, prausnitzii, Pseudoflavonifractor (clade_522 or Pseudoflavonifractor capillosus, Roseburia clade_522i), clade_543 capillosus, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N284.S 9 13 92.3 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus catus, Coprococcus catus, or clade_360c or Coprococcus comes, Dorea Coprococcus comes, clade_360g or clade_360h longicatena, Eubacterium Dorea longicatena, or clade_360i), hallii, Eubacterium rectale, Eubacterium hallii, clade_393, clade_396, Eubacterium siraeum, Eubacterium rectale, (clade_444 or Eubacterium ventriosum, Eubacterium siraeum, clade_444i), (clade_478 Faecalibacterium Eubacterium ventriosum, or clade_478i), prausnitzii, Roseburia Faecalibacterium clade_500, clade_519, intestinalis, Roseburia prausnitzii, Roseburia clade_538 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N271.S 9 13 84.6 92.3 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, (clade_444 or prausnitzii, Holdemania Faecalibacterium clade_444i), (clade_478 filiformis, prausnitzii, Holdemania or clade_478i), Pseudoflavonifractor filiformis, clade_485, clade_494, capillosus, Roseburia Pseudoflavonifractor clade_500, (clade_98 or intestinalis, Roseburia capillosus, Roseburia clade_98i) inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Streptococcus salivarius, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N282.S 9 13 84.6 92.3 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, clade_401, prausnitzii, Holdemania Faecalibacterium (clade_444 or filiformis, Lactococcus prausnitzii, Holdemania clade_444i), (clade_478 lactis, Pseudoflavonifractor filiformis, or clade_478i), capillosus, Roseburia Pseudoflavonifractor clade_485, clade_494, intestinalis, Roseburia capillosus, Roseburia clade_500 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N288.S 8 12 91.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or hallii, Eubacterium rectale, Eubacterium hallii, clade_360g or clade_360h Faecalibacterium Eubacterium rectale, or clade_360i), prausnitzii, Holdemania Faecalibacterium clade_396, (clade_444 or filiformis, prausnitzii, Holdemania clade_444i), (clade_478 Pseudoflavonifractor filiformis, or clade_478i), capillosus, Roseburia Pseudoflavonifractor clade_485, clade_494, intestinalis, Roseburia capillosus, Roseburia clade_500 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N302.S 8 12 91.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus catus, Coprococcus catus, or clade_360c or Coprococcus comes, Dorea Coprococcus comes, clade_360g or clade_360h longicatena, Eubacterium Dorea longicatena, or clade_360i), hallii, Eubacterium rectale, Eubacterium hallii, clade_393, clade_396, Eubacterium ventriosum, Eubacterium rectale, (clade_444 or Faecalibacterium Eubacterium ventriosum, clade_444i), (clade_478 prausnitzii, Roseburia Faecalibacterium or clade_478i), intestinalis, Roseburia prausnitzii, Roseburia clade_500, clade_519 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N279.S 9 12 83.3 100 (clade_172 or Alistipes putredinis, Alistipes putredinis, clade_172i), (clade_262 Bifidobacterium longum, Bifidobacterium longum, or clade_262i), Coprococcus comes, Dorea Coprococcus comes, (clade_360 or clade_360c longicatena, Eubacterium Dorea longicatena, or clade_360g or hallii, Eubacterium rectale, Eubacterium hallii, clade_360h or Faecalibacterium Eubacterium rectale, clade_360i), clade_396, prausnitzii, Holdemania Faecalibacterium (clade_444 or filiformis, prausnitzii, Holdemania clade_444i), (clade_478 Pseudoflavonifractor filiformis, or clade_478i), capillosus, Roseburia Pseudoflavonifractor clade_485, clade_494, inulinivorans, capillosus, Roseburia clade_500 Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N310.S 7 11 90.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, (clade_444 or prausnitzii, Faecalibacterium clade_444i), (clade_478 Pseudoflavonifractor prausnitzii, or clade_478i), capillosus, Roseburia Pseudoflavonifractor clade_494, clade_500 intestinalis, Roseburia capillosus, Roseburia inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N323.S 7 11 90.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus catus, Coprococcus catus, or clade_360c or Coprococcus comes, Dorea Coprococcus comes, clade_360g or clade_360h longicatena, Eubacterium Dorea longicatena, or clade_360i), hallii, Eubacterium rectale, Eubacterium hallii, clade_393, clade_396, Faecalibacterium Eubacterium rectale, (clade_444 or prausnitzii, Roseburia Faecalibacterium clade_444i), (clade_478 intestinalis, Roseburia prausnitzii, Roseburia or clade_478i), clade_500 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N331.S 7 11 90.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Eubacterium siraeum, Eubacterium rectale, clade_396, (clade_444 or Faecalibacterium Eubacterium siraeum, clade_444i), (clade_478 prausnitzii, Roseburia Faecalibacterium or clade_478i), intestinalis, Roseburia prausnitzii, Roseburia clade_500, clade_538 inulinivorans, intestinalis, Roseburia Ruminococcus torques, inulinivorans, Subdoligranulum variabile Ruminococcus torques, Subdoligranulum variabile N332.S 8 11 81.8 90.9 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Holdemania prausnitzii, Holdemania clade_485, clade_494, filiformis, filiformis, clade_500, (clade_98 or Pseudoflavonifractor Pseudoflavonifractor clade_98i) capillosus, Roseburia capillosus, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Streptococcus Subdoligranulum thermophilus, variabile Subdoligranulum variabile N301.S 7 10 90 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, (clade_444 or prausnitzii, Holdemania Faecalibacterium clade_444i), (clade_478 filiformis, Roseburia prausnitzii, Holdemania or clade_478i), intestinalis, Roseburia filiformis, Roseburia clade_485, clade_500 inulinivorans, intestinalis, Roseburia (clade_262 or Ruminococcus torques inulinivorans, Ruminococcus torques N312.S 7 10 90 100 clade_262i), (clade_360 Alistipes putredinis, Alistipes putredinis, or clade_360c or Coprococcus comes, Dorea Coprococcus comes, clade_360g or clade_360h longicatena, Eubacterium Dorea longicatena, or clade_360i), eligens, Eubacterium hallii, Eubacterium eligens, clade_396, (clade_444 or Eubacterium rectale, Eubacterium hallii, clade_444i), (clade_478 Faecalibacterium Eubacterium rectale, or clade_478i), prausnitzii, Roseburia Faecalibacterium clade_500, (clade_ 522 or intestinalis, Roseburia prausnitzii, Roseburia clade_522i) inulinivorans, intestinalis, Roseburia Ruminococcus torques inulinivorans, Ruminococcus torques N339.S 7 10 80 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Coprococcus comes, Coprococcus comes, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_494, clade_500, prausnitzii, Gordonibacter prausnitzii, Gordonibacter (clade_566 or clade_566f) pamelaeae, pamelaeae, Pseudoflavonifractor Pseudoflavonifractor capillosus, Roseburia capillosus, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N325.S 8 10 90 90 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Anaerotruncus Coprococcus comes, or clade_360c or colihominis, Coprococcus Dorea longicatena, clade_360g or clade_360h comes, Dorea longicatena, Eubacterium hallii, or clade_360i), Eubacterium hallii, Eubacterium rectale, clade_396, (clade_444 or Eubacterium rectale, Faecalibacterium clade_444i), (clade_478 Faecalibacterium prausnitzii, or clade_478i), prausnitzii, Pseudoflavonifractor clade_494, clade_500, Pseudoflavonifractor capillosus, Ruminococcus (clade_516 or clade_516c capillosus, Ruminococcus torques, Subdoligranulum or clade_516g or torques, Subdoligranulum variabile clade_516h) variabile N340.S 7 10 90 90 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_354 Clostridium bartlettii, Eubacterium hallii, or clade_354e), Eubacterium hallii, Eubacterium rectale, clade_396, (clade_444 or Eubacterium rectale, Faecalibacterium clade_444i), (clade_478 Faecalibacterium prausnitzii, or clade_478i), prausnitzii, Pseudoflavonifractor clade_494, clade_500 Pseudoflavonifractor capillosus, Roseburia capillosus, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N341.S 7 10 90 90 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Anaerotruncus Eubacterium hallii, (clade_444 or colihominis, Eubacterium Eubacterium rectale, clade_444i), (clade_478 hallii, Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, clade_494, clade_500, prausnitzii, Pseudoflavonifractor (clade_516 or clade_516c Pseudoflavonifractor capillosus, Roseburia or clade_516g or capillosus, Roseburia intestinalis, Roseburia clade_516h) intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N346.S 7 10 90 90 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Holdemania prausnitzii, Holdemania clade_485, clade_500, filiformis, Roseburia filiformis, Roseburia (clade_516 or clade_516c intestinalis, Roseburia intestinalis, Roseburia or clade_516g or inulinivorans, inulinivorans, clade_516h) Ruminococcus albus, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N338.S 7 10 80 90 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium eligens, Eubacterium eligens, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_500, (clade_522 or prausnitzii, Roseburia prausnitzii, Roseburia clade_522i), (clade_98 or intestinalis, Roseburia intestinalis, Roseburia clade_98i) inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Streptococcus australis, Subdoligranulum Subdoligranulum variabile variabile N336.S 6 9 88.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, (clade_444 or prausnitzii, Roseburia Faecalibacterium clade_444i), (clade_478 intestinalis, Roseburia prausnitzii, Roseburia or clade_478i), clade_500 inulinivorans, intestinalis, Roseburia Ruminococcus torques inulinivorans, Ruminococcus torques N345.S 7 9 88.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i) prausnitzii, Holdemania prausnitzii, Holdemania clade_485, clade_494, filiformis, filiformis, clade_500 Pseudoflavonifractor Pseudoflavonifractor capillosus, Roseburia capillosus, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N355.S 6 9 88.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Eubacterium ventriosum, Eubacterium ventriosum, or clade_478i), Faecalibacterium Faecalibacterium clade_500, clade_519 prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N356.S 6 9 88.9 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Coprococcus comes, Coprococcus comes, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_500, clade_537 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus bromii, Ruminococcus bromii, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N343.S 7 9 77.8 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_286, Coprococcus comes, Dorea Coprococcus comes, (clade_360 or clade_360c longicatena, Eubacterium Dorea longicatena, or clade_360g or hallii, Eubacterium rectale, Eubacterium hallii, clade_360h or Faecalibacterium Eubacterium rectale, clade_360i), clade_396, prausnitzii, Faecalibacterium (clade_444 or Parabacteroides merdae, prausnitzii, clade_444i), (clade_478 Roseburia inulinivorans, Parabacteroides merdae, or clade_478i), clade_500 Ruminococcus torques Roseburia inulinivorans, Ruminococcus torques N329.S 6 9 88.9 88.9 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Collinsella aerofaciens, Eubacterium hallii, (clade_444 or Eubacterium hallii, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, Roseburia clade_500, (clade_553 or prausnitzii, Roseburia intestinalis, Roseburia clade_553i) intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N361.S 6 9 88.9 88.9 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Roseburia prausnitzii, Roseburia clade_500, (clade_516 or intestinalis, Roseburia intestinalis, Roseburia clade_516c or clade_516g inulinivorans, inulinivorans, or clade_516h) Ruminococcus albus, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N353.S 7 9 77.8 88.9 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Dialister invisus, Eubacterium hallii, (clade_444 or Eubacterium hallii, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, clade_494, clade_500, prausnitzii, Pseudoflavonifractor clade_506 Pseudoflavonifractor capillosus, Roseburia capillosus, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum Subdoligranulum variabile variabile N381.S 7 9 100 77.8 (clade_262 or Anaerotruncus Clostridium leptum, clade_262i), (clade_444 colihominis, Clostridium Eubacterium eligens, or clade_444i), leptum, Clostridium Faecalibacterium (clade_478 or methylpentosum, prausnitzii, clade_478i), clade_494, Eubacterium eligens, Pseudoflavonifractor (clade_516 or clade_516c Faecalibacterium capillosus, Roseburia or clade_516g or prausnitzii, intestinalis, Roseburia clade_516h), (clade_522 Pseudoflavonifractor inulinivorans, or clade_522i), clade_537 capillosus, Roseburia Ruminococcus torques intestinalis, Roseburia inulinivorans, Ruminococcus torques N344.S 6 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Eubacterium rectale, Eubacterium hallii, or clade_360i), Faecalibacterium Eubacterium rectale, clade_396, (clade_444 or prausnitzii, Roseburia Faecalibacterium clade_444i), (clade_478 inulinivorans, prausnitzii, Roseburia or clade_478i), clade_500 Ruminococcus torques inulinivorans, Ruminococcus torques N352.S 5 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N357.S 6 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Holdemania prausnitzii, Holdemania clade_485, clade_500 filiformis, Roseburia filiformis, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N358.S 5 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Coprococcus comes, Coprococcus comes, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N369.S 6 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium eligens, Eubacterium eligens, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_500, (clade_522 or prausnitzii, Roseburia prausnitzii, Roseburia clade_522i) intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N372.S 6 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, prausnitzii, clade_494, clade_500 Pseudoflavonifractor Pseudoflavonifractor capillosus, Roseburia capillosus, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N375.S 6 8 87.5 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Clostridium leptum, Clostridium leptum, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_500, clade_537 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N380.S 7 8 87.5 100 (clade_262 or Bacteroides ovatus, Dorea Bacteroides ovatus, Dorea clade_262i), (clade_360 longicatena, Eubacterium longicatena, Eubacterium or clade_360c or eligens, Eubacterium eligens, Eubacterium clade_360g or clade_360h rectale, Eubacterium rectale, Eubacterium or clade_360i), (clade_38 ventriosum, ventriosum, or clade_38e or Faecalibacterium Faecalibacterium clade_38i), (clade_444 or prausnitzii, Roseburia prausnitzii, Roseburia clade_444i), (clade_478 intestinalis, Ruminococcus intestinalis, or clade_478i), torques Ruminococcus torques clade_519, (clade_522 or clade_522i) N374.S 6 8 75 100 (clade_172 or Alistipes putredinis, Alistipes putredinis, clade_172i), (clade_262 Bifidobacterium longum, Bifidobacterium longum, or clade_262i), Coprococcus comes, Coprococcus comes, clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N377.S 6 8 75 100 clade_170, (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Bacteroides caccae, Bacteroides caccae, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N368.S 6 8 75 87.5 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Roseburia prausnitzii, Roseburia clade_500, (clade_98 or intestinalis, Roseburia intestinalis, Roseburia clade_98i) inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques Streptococcus salivarius N370.S 5 7 85.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Coprococcus comes, Coprococcus comes, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N373.S 6 7 85.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Holdemania prausnitzii, Holdemania clade_485, clade_500 filiformis, Roseburia filiformis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N376.S 5 7 85.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N389.S 6 7 85.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_393, Coprococcus catus, Coprococcus catus, clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N394.S 5 7 85.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_ 444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N431.S 6 7 85.7 100 (clade_262 or Bacteroides ovatus, Dorea Bacteroides ovatus, Dorea clade_262i), (clade_360 longicatena, Eubacterium longicatena, Eubacterium or clade_360c or rectale, Eubacterium rectale, Eubacterium clade_360g or clade_360h ventriosum, ventriosum, or clade_360i), (clade_38 Faecalibacterium Faecalibacterium or clade_38e or prausnitzii, Roseburia prausnitzii, Roseburia clade_38i), (clade_444 or intestinalis, Ruminococcus intestinalis, clade_444i), (clade_478 torques Ruminococcus torques or clade_478i), clade_519 N434.S 6 7 85.7 100 (clade_262 or Bacteroides ovatus, Dorea Bacteroides ovatus, Dorea clade_262i), (clade_360 longicatena, Eubacterium longicatena, Eubacterium or clade_360c or eligens, Eubacterium eligens, Eubacterium clade_360g or clade_360h rectale, Faecalibacterium rectale, Faecalibacterium or clade_360i), (clade_38 prausnitzii, Roseburia prausnitzii, Roseburia or clade_38e or intestinalis, Ruminococcus intestinalis, clade_38i), (clade_444 or torques Ruminococcus torques clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N390.S 6 7 71.4 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Bilophila wadsworthia, Bilophila wadsworthia, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i), Faecalibacterium Faecalibacterium clade_500, clade_521 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N397.S 6 7 71.4 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_38 or Bacteroides ovatus, Bacteroides ovatus, clade_38e or clade_38i), Eubacterium hallii, Eubacterium hallii, clade_396, (clade_444 or Eubacterium_rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N387.S 6 7 85.7 85.7 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Collinsella aerofaciens, Eubacterium hallii, (clade_444 or Eubacterium hallii, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, Roseburia clade_500, (clade_553 or prausnitzii, Roseburia inulinivorans, clade_553i) inulinivorans, Ruminococcus torques Ruminococcus torques N440.S 7 7 85.7 85.7 (clade_262 or Clostridium leptum, Clostridium leptum, clade_262i), (clade_408 Clostridium symbiosum, Desulfovibrio or clade_408b or Desulfovibrio desulfuricans, clade_408d or clade_408f desulfuricans, Eubacterium Eubacterium rectale, or clade_408g or rectale, Faecalibacterium Faecalibacterium clade_408h), (clade_444 prausnitzii, prausnitzii, or clade_444i), Pseudoflavonifractor Pseudoflavonifractor clade_445, (clade_478 or capillosus, Ruminococcus capillosus, Ruminococcus clade_478i), clade_494, torques torques clade_537 N396.S 6 7 71.4 85.7 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Bacteroides fragilis, Eubacterium hallii, (clade_444 or Eubacterium hallii, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, Roseburia clade_500, (clade_65 or prausnitzii, Roseburia inulinivorans, clade_65e) inulinivorans, Ruminococcus torques Ruminococcus torques N399.S 6 6 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium hallii, Eubacterium hallii, or clade_360c or Eubacterium rectale, Eubacterium rectale, clade_360g or clade_360h Faecalibacterium Faecalibacterium or clade_360i), prausnitzii, prausnitzii, clade_396, (clade_444 or Pseudoflavonifractor Pseudoflavonifractor clade_444i), (clade_478 capillosus, Ruminococcus capillosus, Ruminococcus or clade_478i), clade_494 torques torques N403.S 4 6 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or rectale, Faecalibacterium Eubacterium rectale, clade_360g or clade_360h prausnitzii, Roseburia Faecalibacterium or clade_360i), intestinalis, Ruminococcus prausnitzii, Roseburia (clade_444 or torques intestinalis, clade_444i), (clade_478 Ruminococcus torques or clade_478i) N414.S 5 6 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or eligens, Eubacterium Eubacterium eligens, clade_360g or clade_360h rectale, Faecalibacterium Eubacterium rectale, or clade_360i), prausnitzii, Ruminococcus Faecalibacterium (clade_444 or torques prausnitzii, clade_444i), (clade_478 Ruminococcus torques or clade_478i), (clade_522 or clade_522i) N430.S 6 6 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium eligens, Eubacterium eligens, or clade_360c or Eubacterium rectale, Eubacterium rectale, clade_360g or clade_360h Eubacterium ventriosum, Eubacterium ventriosum, or clade_360i), Faecalibacterium Faecalibacterium (clade_444 or prausnitzii, Ruminococcus prausnitzii, clade_444i), (clade_478 torques Ruminococcus torques or clade_478i), clade_519, (clade_522 or clade_522i) N432.S 4 6 100 100 (clade_262 or Clostridium leptum, Clostridium leptum, clade_262i), (clade_444 Coprococcus comes, Coprococcus comes, or clade_444i), Eubacterium rectale, Eubacterium rectale, (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_537 prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Ruminococcus intestinalis, torques Ruminococcus torques N436.S 4 6 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or hallii, Eubacterium rectale, Eubacterium hallii, clade_360g or clade_360h Roseburia inulinivorans, Eubacterium rectale, or clade_360i), Ruminococcus torques Roseburia inulinivorans, clade_396, (clade_444 or Ruminococcus torques clade_444i) N437.S 3 6 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques, Ruminococcus torques, Subdoligranulum variabile Subdoligranulum variabile N457.S 5 6 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium eligens, Eubacterium eligens, or clade_360c or Eubacterium rectale, Eubacterium rectale, clade_360g or clade_360h Faecalibacterium Faecalibacterium or clade_360i), prausnitzii, Roseburia prausnitzii, Roseburia (clade_444 or intestinalis, Ruminococcus intestinalis, clade_444i), (clade_478 torques Ruminococcus torques or clade_478i), (clade_522 or clade_522i) N545 5 6 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or hallii, Eubacterium Eubacterium hallii, clade_360g or clade_360h siraeum, Roseburia Eubacterium siraeum, or clade_360i), intestinalis, Roseburia Roseburia intestinalis, clade_396, (clade_444 or inulinivorans Roseburia inulinivorans clade_444i), clade_538 N386.S 5 6 83.3 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N402.S 5 6 83.3 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), clade_286, longicatena, Eubacterium Dorea longicatena, (clade_360 or clade_360c rectale, Faecalibacterium Eubacterium rectale, or clade_360g or prausnitzii, Faecalibacterium clade_360h or Parabacteroides merdae, prausnitzii, clade_360i), (clade_444 Ruminococcus torques Parabacteroides merdae, or clade_444i), Ruminococcus torques (clade_478 or clade_478i) N405.S 4 6 83.3 100 (clade_262 or Desulfovibrio Desulfovibrio clade_262i), (clade_444 desulfuricans, Eubacterium desulfuricans, or clade_444i), rectale, Faecalibacterium Eubacterium rectale, clade_445, (clade_478 or prausnitzii, Roseburia Faecalibacterium clade_478i) intestinalis, Ruminococcus prausnitzii, Roseburia torques, Subdoligranulum intestinalis, variabile Ruminococcus torques, Subdoligranulum variabile N415.S 5 6 83.3 100 clade_170, (clade_262 or Bacteroides caccae, Bacteroides caccae, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h rectale, Faecalibacterium Eubacterium rectale, or clade_360i), prausnitzii, Ruminococcus Faecalibacterium (clade_444 or torques prausnitzii, clade_444i), (clade_478 Ruminococcus torques or clade_478i) N421.S 6 6 83.3 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Roseburia Eubacterium hallii, or clade_360i), inulinivorans, Roseburia inulinivorans, clade_396, (clade_444 or Subdoligranulum variabile Subdoligranulum clade_444i), (clade_478 variabile or clade_478i), clade_500 N422.S 5 6 83.3 100 (clade_262 or Alistipes putredinis, Dorea Alistipes putredinis, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or rectale, Eubacterium rectale, clade_360g or clade_360h Pseudoflavonifractor Pseudoflavonifractor or clade_360i), capillosus, Roseburia capillosus, Roseburia (clade_444 or intestinalis, Ruminococcus intestinalis, clade_444i), clade_494, torques Ruminococcus torques clade_500 N423.S 5 6 83.3 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Eubacterium siraeum, Eubacterium siraeum, (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_500, prausnitzii, Ruminococcus prausnitzii, clade_538 torques, Subdoligranulum Ruminococcus torques, variabile Subdoligranulum variabile N458.S 6 6 83.3 100 (clade_262 or Bacteroides ovatus, Dorea Bacteroides ovatus, Dorea clade_262i), (clade_360 longicatena, Eubacterium longicatena, Eubacterium or clade_360c or eligens, Eubacterium eligens, Eubacterium clade_360g or clade_360h rectale, Faecalibacterium rectale, Faecalibacterium or clade_360i), (clade_38 prausnitzii, Ruminococcus prausnitzii, or clade_38e or torques Ruminococcus torques clade_38i), (clade_444 or clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N459.S 5 6 83.3 100 (clade_262 or Bacteroides ovatus, Dorea Bacteroides ovatus, Dorea clade_262i), (clade_360 longicatena, Eubacterium longicatena, Eubacterium or clade_360c or rectale, Faecalibacterium rectale, Faecalibacterium clade_360g or clade_360h prausnitzii, Roseburia prausnitzii, Roseburia or clade_360i), (clade_38 intestinalis, Ruminococcus intestinalis, or clade_38e or torques Ruminococcus torques clade_38i), (clade_444 or clade_444i), (clade_478 or clade_478i) N493.S 6 6 100 83.3 (clade_262 or Clostridium bartlettii, Eubacterium hallii, clade_262i), (clade_354 Eubacterium hallii, Eubacterium rectale, or clade_354e), Eubacterium rectale, Faecalibacterium clade_396, (clade_444 or Faecalibacterium prausnitzii, clade_444i), (clade_478 prausnitzii, Pseudoflavonifractor or clade_478i), clade_494 Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N416.S 6 6 83.3 83.3 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Anaerotruncus Eubacterium hallii, (clade_444 or colihominis, Eubacterium Eubacterium rectale, clade_444i), clade_494, hallii, Eubacterium rectale, Pseudoflavonifractor clade_500, (clade_516 or Pseudoflavonifractor capillosus, Ruminococcus clade_516c or clade_516g capillosus, Ruminococcus torques or clade_516h) torques N439.S 6 6 83.3 83.3 (clade_262 or Bifidobacterium bifidum, Dorea longicatena, clade_262i), clade_293, Dorea longicatena, Eubacterium rectale, (clade_360 or clade_360c Eubacterium rectale, Faecalibacterium or clade_360g or Faecalibacterium prausnitzii, clade_360h or prausnitzii, Pseudoflavonifractor clade_360i), (clade_444 Pseudoflavonifractor capillosus, Ruminococcus or clade_444i), capillosus, Ruminococcus torques (clade_478 or torques clade_478i), clade_494 N447.S 5 6 83.3 83.3 (clade_262 or Dialister invisus, Eubacterium rectale, clade_262i), (clade_444 Eubacterium rectale, Faecalibacterium or clade_444i), Faecalibacterium prausnitzii, (clade_478 or prausnitzii, Pseudoflavonifractor clade_478i), clade_494, Pseudoflavonifractor capillosus, Ruminococcus clade_506 capillosus, Ruminococcus torques, Subdoligmnulum torques, Subdoligranulum variabile variabile N490.S 5 6 83.3 83.3 (clade_262 or Eubacterium hallii, Eubacterium hallii, clade_262i), clade_396, Eubacterium rectale, Eubacterium rectale, (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i), (clade_98 intestinalis, Ruminococcus intestinalis, or clade_98i) torques, Streptococcus Ruminococcus torques australis N526 5 6 83.3 83.3 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), clade_271, longicatena, Eubacterium Dorea longicatena, (clade_360 or clade_360c hallii, Roseburia Eubacterium hallii, or clade_360g or intestinalis, Roseburia Roseburia intestinalis, clade_360h or inulinivorans, Rothia Roseburia inulinivorans clade_360i), clade_396, (clade_444 or clade_444i) N429.S 4 5 100 100 (clade_444 or Eubacterium eligens, Eubacterium eligens, clade_444i), (clade_478 Eubacterium ventriosum, Eubacterium ventriosum, or clade_478i), Faecalibacterium Faecalibacterium clade_519, (clade_522 or prausnitzii, Roseburia prausnitzii, Roseburia clade_522i) inulinivorans, inulinivorans, Subdoligranulum variabile Subdoligranulum variabile N433.S 4 5 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or rectale, Faecalibacterium Eubacterium rectale, clade_360g or clade_360h prausnitzii, Ruminococcus Faecalibacterium or clade_360i), torques prausnitzii, (clade_444 or Ruminococcus torques clade_444i), (clade_478 or clade_478i) N448.S 4 5 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i) inulinivorans, inulinivorans, Subdoligranulum variabile Subdoligranulum variabile N488.S 4 5 100 100 (clade_262 or Eubacterium hallii, Eubacterium hallii, clade_262i), clade_396, Eubacterium rectale, Eubacterium rectale, (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i) intestinalis, Ruminococcus intestinalis, torques Ruminococcus torques N508.S 4 5 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium rectale, Eubacterium rectale, or clade_360c or Faecalibacterium Faecalibacterium clade_360g or clade_360h prausnitzii, Roseburia prausnitzii, Roseburia or clade_360i), intestinalis, Ruminococcus intestinalis, (clade_444 or torques Ruminococcus torques clade_444i), (clade_478 or clade_478i) N509.S 5 5 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium rectale, Eubacterium rectale, or clade_360c or Eubacterium ventriosum, Eubacterium ventriosum, clade_360g or clade_360h Faecalibacterium Faecalibacterium or clade_360i), prausnitzii, Ruminococcus prausnitzii, (clade_444 or torques Ruminococcus torques clade_444i), (clade_478 or clade_478i), clade_519 N510.S 5 5 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium eligens, Eubacterium eligens, or clade_360c or Eubacterium rectale, Eubacterium rectale, clade_360g or clade_360h Faecalibacterium Faecalibacterium or clade_360i), prausnitzii, Ruminococcus prausnitzii, (clade_444 or torques Ruminococcus torques clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N511.S 3 5 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Ruminococcus intestinalis, torques Ruminococcus torques N408.S 5 5 80 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Eubacterium eligens, Eubacterium eligens, or clade_478i), Faecalibacterium Faecalibacterium clade_494, clade_500, prausnitzii, prausnitzii, (clade_522 or clade_522i) Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N446.S 5 5 80 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii, Roseburia Eubacterium hallii, or clade_360i), inulinivorans Roseburia inulinivorans clade_396, (clade_444 or clade_444i), clade_500 N451.S 4 5 80 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Coprococcus comes, Coprococcus comes, (clade_478 or Eubacterium hallii, Eubacterium hallii, clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N474.S 5 5 80 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, Gordonibacter prausnitzii, Gordonibacter (clade_478 or pamelaeae, pamelaeae, clade_478i), clade_494, Pseudoflavonifractor Pseudoflavonifractor (clade_566 or clade_566f) capillosus, Ruminococcus capillosus, Ruminococcus torques torques N520.S 5 5 80 100 (clade_262 or Clostridium leptum, Clostridium leptum, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Gordonibacter prausnitzii, Gordonibacter clade_494, clade_537, pamelaeae, pamelaeae, (clade_566 or clade_566f) Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N521.S 5 5 80 100 (clade_262 or Coprococcus catus, Coprococcus catus, clade_262i), clade_393, Desulfovibrio Desulfovibrio (clade_444 or desulfuricans, desulfuricans, clade_444i), clade_445, Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii, Roseburia prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N535.S 4 5 80 100 clade_358, clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i) inulinivorans, inulinivorans, Subdoligranulum variabile, Subdoligranulum Veillonella atypica variabile, Veillonella atypica N516.S 5 5 60 100 clade_393, (clade_444 or Bilophila wadsworthia, Bilophila wadsworthia, clade_444i), clade_445, Coprococcus catus, Coprococcus catus, clade_521, (clade_522 or Desulfovibrio Desulfovibrio clade_522i) desulfuricans, Eubacterium desulfuricans, eligens, Eubacterium Eubacterium eligens, rectale Eubacterium rectale N463.S 5 5 100 80 clade_246, (clade_262 or Clostridiales sp. SS3/4, Clostridium clade_262i), (clade_444 Clostridium lactatifermentans, or clade_444i), lactatifermentans, Faecalibacterium (clade_478 or Faecalibacterium prausnitzii, Roseburia clade_478i), clade_576 prausnitzii, Roseburia inulinivorans, inulinivorans, Ruminococcus torques Ruminococcus torques N518.S 5 5 100 80 (clade_262 or Clostridium bartlettii, Eubacterium hallii, clade_262i), (clade_354 Eubacterium hallii, Eubacterium rectale, or clade_354e), Eubacterium rectale, Pseudoflavonifractor clade_396, (clade_444 or Pseudoflavonifractor capillosus, Ruminococcus clade_444i), clade_494 capillosus, Ruminococcus torques torques N586 3 5 100 80 clade_368, (clade_444 or Blautia hydrogenotrophica, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Roseburia intestinalis, or clade_478i) Roseburia intestinalis, Roseburia inulinivorans, Roseburia inulinivorans, Subdoligranulum Subdoligranulum variabile variabile N450.S 5 5 80 80 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Anaerotruncus Faecalibacterium or clade_478i), colihominis, prausnitzii, clade_494, clade_500, Faecalibacterium Pseudoflavonifractor (clade_516 or clade_516c prausnitzii, capillosus, Ruminococcus or clade_516g or Pseudoflavonifractor torques clade_516h) capillosus, Ruminococcus torques N465.S 4 5 80 80 clade_168, (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, Prevotella prausnitzii, Roseburia (clade_478 or clade_478i) copri, Roseburia intestinalis, intestinalis, Ruminococcus Ruminococcus torques torques N519.S 5 5 80 80 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), clade_401, Faecalibacterium Faecalibacterium (clade_444 or prausnitzii, Lactococcus prausnitzii, clade_444i), (clade_478 lactis, Pseudoflavonifractor Pseudoflavonifractor or clade_478i), clade_494 capillosus, Ruminococcus capillosus, Ruminococcus torques torques N537.S 5 5 80 80 (clade_260 or clade_260c Clostridium scindens, Desulfovibrio or clade_260g or Desulfovibrio desulfuricans, clade_260h), (clade_262 desulfuricans, Eubacterium Eubacterium rectale, or clade_262i), rectale, Pseudoflavonifractor (clade_444 or Pseudoflavonifractor capillosus, Ruminococcus clade_444i), clade_445, capillosus, Ruminococcus torques clade_494 torques N419.S 5 5 60 80 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Pseudoflavonifractor Pseudoflavonifractor clade_494, clade_500, capillosus, Ruminococcus capillosus, Ruminococcus (clade_98 or clade_98i) torques, Streptococcus torques salivarius N468.S 5 5 60 80 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_293, Bifidobacterium bifidum, Coprococcus comes, (clade_360 or clade_360c Coprococcus comes, Dorea Dorea longicatena, or clade_360g or longicatena, Eubacterium Eubacterium hallii clade_360h or hallii clade_360i), clade_396, clade_500 N477.S 5 5 60 80 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Pseudoflavonifractor Pseudoflavonifractor clade_494, clade_500, capillosus, Ruminococcus capillosus, Ruminococcus (clade_98 or clade_98i) torques, Streptococcus torques thermophilus N514.S 5 5 60 60 clade_393, (clade_420 or Clostridiales bacterium Coprococcus catus, clade_420f), (clade_444 oral clone P4PA, Eubacterium eligens, or clade_444i), Coprococcus catus, Eubacterium rectale (clade_522 or Eubacterium eligens, clade_522i), clade_558 Eubacterium rectale, Tannerella sp. 6_1_58FAA_CT1 N382.S 5 5 100 40 (clade_260 or clade_260c Clostridium hylemonae, Coprococcus comes, or clade_260g or Clostridium symbiosum, Ruminococcus bromii clade_260h), (clade_262 Collinsella aerofaciens, or clade_262i), Coprococcus comes, (clade_408 or clade_408b Ruminococcus bromii or clade_408d or clade_408f or clade_408g or clade_408h), clade_537, (clade_553 or clade_553i) N460.S 3 4 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N462.S 3 4 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Dorea longicatena, or clade_360c or Faecalibacterium Faecalibacterium clade_360g or clade_360h prausnitzii, prausnitzii, or clade_360i), Subdoligranulum variabile Subdoligranulum (clade_478 or clade_478i) variabile N512.S 3 4 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or rectale, Ruminococcus Eubacterium rectale, clade_360g or clade_360h torques Ruminococcus torques or clade_360i), (clade_444 or clade_444i) N517.S 4 4 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Eubacterium rectale, Eubacterium rectale, or clade_360c or Faecalibacterium Faecalibacterium clade_360g or clade_360h prausnitzii, Ruminococcus prausnitzii, or clade_360i), torques Ruminococcus torques (clade_444 or clade_444i), (clade_478 or clade_478i) N523.S 3 4 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, Roseburia prausnitzii, Roseburia (clade_478 or clade_478i) intestinalis, Ruminococcus intestinalis, torques Ruminococcus torques N547.S 3 4 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, Ruminococcus prausnitzii, (clade_478 or clade_478i) torques, Subdoligranulum Ruminococcus torques, variabile Subdoligranulum variabile N548.S 4 4 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, prausnitzii, (clade_478 or Pseudoflavonifractor Pseudoflavonifractor clade_478i), clade_494 capillosus, Ruminococcus capillosus, Ruminococcus torques torques N577.S 3 4 100 100 (clade_262 or Clostridium leptum, Clostridium leptum, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Dorea longicatena, clade_360g or clade_360h Ruminococcus torques Ruminococcus torques or clade_360i), clade_537 N581.S 4 4 100 100 (clade_262 or Eubacterium siraeum, Eubacterium siraeum, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, prausnitzii, clade_494, clade_538 Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N585.S 2 4 100 100 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i) prausnitzii, Roseburia prausnitzii, Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans inulinivorans N616.S 4 4 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or hallii, Faecalibacterium Eubacterium hallii, clade_360g or clade_360h prausnitzii Faecalibacterium or clade_360i), prausnitzii clade_396, (clade_478 or clade_478i) N466.S 4 4 75 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Pseudoflavonifractor Pseudoflavonifractor clade_494, clade_500 capillosus, Ruminococcus capillosus, Ruminococcus torques torques N469.S 4 4 75 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena, Eubacterium Dorea longicatena, clade_360g or clade_360h hallii Eubacterium hallii or clade_360i), clade_396, clade_500 N480.S 4 4 75 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Ruminococcus prausnitzii, clade_500, clade_537 bromii, Ruminococcus Ruminococcus bromii, torques Ruminococcus torques N482.S 4 4 75 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Eubacterium eligens, Eubacterium eligens, or clade_478i), Faecalibacterium Faecalibacterium clade_500, (clade_522 or prausnitzii, Ruminococcus prausnitzii, clade_522i) torques Ruminococcus torques N484.S 4 4 75 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_500 prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N515.S 4 4 75 100 clade_393, (clade_444 or Bilophila wadsworthia, Bilophila wadsworthia, clade_444i), clade_521, Coprococcus catus, Coprococcus catus, (clade_522 or clade_522i) Eubacterium eligens, Eubacterium eligens, Eubacterium rectale Eubacterium rectale N533.S 4 4 75 100 (clade_262 or Desulfovibrio Desulfovibrio clade_262i), (clade_444 desulfuricans, Eubacterium desulfuricans, or clade_444i), rectale, Eubacterium rectale, clade_445, clade_494 Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N709 4 4 75 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or Gordonibacter pamelaeae, Gordonibacter pamelaeae, clade_444i), (clade_566 Roseburia inulinivorans Roseburia inulinivorans or clade_566f) N730 4 4 75 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_286, Eubacterium hallii, Eubacterium hallii, clade_396, (clade_444 or Parabacteroides merdae, Parabacteroides merdae, clade_444i) Roseburia inulinivorans Roseburia inulinivorans N478.S 4 4 50 100 clade_170, (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Bacteroides caccae, Bacteroides caccae, or clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N572.S 4 4 50 100 clade_286, (clade_444 or Desulfovibrio Desulfovibrio clade_444i), clade_445, desulfuricans, Eubacterium desulfuricans, (clade_478 or clade_478i) rectale, Faecalibacterium Eubacterium rectale, prausnitzii, Faecalibacterium Parabacteroides merdae prausnitzii, Parabacteroides merdae N400.S 4 4 100 75 (clade_262 or Clostridium symbiosum, Coprococcus comes, clade_262i), (clade_408 Coprococcus comes, Eubacterium rectale, or clade_408b or Eubacterium rectale, Faecalibacterium clade_408d or clade_408f Faecalibacterium prausnitzii or clade_408g or prausnitzii clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i) N543.S 4 4 100 75 (clade_262 or Clostridium bartlettii, Faecalibacterium clade_262i), (clade_354 Faecalibacterium prausnitzii, or clade_354e), prausnitzii, Pseudoflavonifractor (clade_478 or Pseudoflavonifractor capillosus, Ruminococcus clade_478i), clade_494 capillosus, Ruminococcus torques torques N582.S 4 4 100 75 (clade_262 or Clostridium symbiosum, Eubacterium rectale, clade_262i), (clade_408 Eubacterium rectale, Faecalibacterium or clade_408b or Faecalibacterium prausnitzii, clade_408d or clade_408f prausnitzii, Ruminococcus Ruminococcus torques or clade_408g or torques clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i) N621.S 4 4 100 75 clade_396, (clade_408 or Anaerostipes caccae, Eubacterium hallii, clade_408b or clade_408d Eubacterium hallii, Eubacterium rectale, or clade_408f or Eubacterium rectale, Faecalibacterium clade_408g or Faecalibacterium prausnitzii clade_408h), (clade_444 prausnitzii or clade_444i), (clade_478 or clade_478i) N689 4 4 100 75 (clade_262 or Clostridium Coprococcus comes, clade_262i), clade_396, methylpentosum, Eubacterium hallii, (clade_444 or Coprococcus comes, Roseburia inulinivorans clade_444i), (clade_516 Eubacterium hallii, or clade_516c or Roseburia inulinivorans clade_516g or clade_516h) N769 4 4 100 75 (clade_260 or clade_260c Clostridium scindens, Faecalibacterium or clade_260g or Faecalibacterium prausnitzii, clade_260h), (clade_262 prausnitzii, Pseudoflavonifractor or clade_262i), Pseudoflavonifractor capillosus, Ruminococcus (clade_478 or capillosus, Ruminococcus torques clade_478i), clade_494 torques N481.S 4 4 75 75 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Collinsella aerofaciens, Faecalibacterium or clade_478i), Faecalibacterium prausnitzii, clade_500, (clade_553 or prausnitzii, Ruminococcus Ruminococcus torques clade_553i) torques N525.S 4 4 75 75 (clade_262 or Anaerostipes caccae, Desulfovibrio clade_262i), (clade_408 Desulfovibrio desulfuricans, or clade_408b or desulfuricans, Pseudoflavonifractor clade_408d or clade_408f Pseudoflavonifractor capillosus, Ruminococcus or clade_408g or capillosus, Ruminococcus torques clade_408h), clade_445, torques clade_494 N528.S 4 4 75 75 (clade_262 or Clostridium symbiosum, Desulfovibrio clade_262i), (clade_408 Desulfovibrio desulfuricans, or clade_408b or desulfuricans, Pseudoflavonifractor clade_408d or clade_408f Pseudoflavonifractor capillosus, Ruminococcus or clade_408g or capillosus, Ruminococcus torques clade_408h), clade_445, torques clade_494 N534.S 4 4 75 75 (clade_262 or Bacteroides fragilis, Eubacterium rectale, clade_262i), (clade_444 Eubacterium rectale, Faecalibacterium or clade_444i), Faecalibacterium prausnitzii, (clade_478 or prausnitzii, Ruminococcus Ruminococcus torques clade_478i), (clade_65 or torques clade_65e) N574.S 4 4 75 75 clade_396, (clade_478 or Clostridium leptum, Clostridium leptum, clade_478i), clade_537, Eubacterium hallii, Eubacterium hallii, (clade_98 or clade_98i) Faecalibacterium Faecalibacterium prausnitzii, Streptococcus prausnitzii thermophilus N580.S 4 4 75 75 (clade_262 or Eubacterium hallii, Eubacterium hallii, clade_262i), clade_396, Eubacterium rectale, Eubacterium rectale, (clade_444 or Ruminococcus torques, Ruminococcus torques clade_444i), (clade_98 or Streptococcus australis clade_98i) N590.S 3 4 75 75 clade_401, (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_485 prausnitzii, Holdemania prausnitzii, Holdemania filiformis, Lactococcus filiformis, lactis, Subdoligranulum Subdoligranulum variabile variabile N591.S 4 4 75 75 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), clade_401, Lactococcus lactis, Pseudoflavonifractor (clade_444 or Pseudoflavonifractor capillosus, Ruminococcus clade_444i), clade_494 capillosus, Ruminococcus torques torques N597.S 3 4 75 75 (clade_478 or Eubacterium eligens, Eubacterium eligens, clade_478i), (clade_522 Faecalibacterium Faecalibacterium or clade_522i), (clade_98 prausnitzii, Streptococcus prausnitzii, or clade_98i) australis, Subdoligranulum Subdoligranulum variabile variabile N664 4 4 75 75 (clade_360 or clade_360c Bacteroides dorei, Bacteroides dorei, Dorea or clade_360g or Clostridium longicatena, Eubacterium clade_360h or methylpentosum, Dorea ventriosum clade_360i), (clade_378 longicatena, Eubacterium or clade_378e), ventriosum (clade_516 or clade_516c or clade_516g or clade_516h), clade_519 N693 4 4 75 75 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, clade_401, (clade_444 or Lactococcus lactis, Roseburia inulinivorans clade_444i) Roseburia inulinivorans N530.S 4 4 50 75 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), Ruminococcus torques, Ruminococcus torques clade_500, (clade_98 or Streptococcus australis clade_98i) N687 4 4 100 50 clade_396, (clade_444 or Bacteroides pectinophilus, Faecalibacterium clade_444i), (clade_478 Coprococcus eutactus, prausnitzii, Roseburia or clade_478i), clade_543 Faecalibacterium intestinalis prausnitzii, Roseburia intestinalis N470.S 2 3 100 100 (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_485 prausnitzii, Holdemania prausnitzii, Holdemania filiformis, filiformis, Subdoligranulum variabile Subdoligranulum variabile N529.S 3 3 100 100 (clade_262 or Faecalibacterium Faecalibacterium clade_262i), (clade_478 prausnitzii, prausnitzii, or clade_478i), clade_494 Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N539.S 2 3 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Roseburia intestinalis, Roseburia intestinalis, or clade_444i) Ruminococcus torques Ruminococcus torques N546.S 3 3 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Faecalibacterium Faecalibacterium or clade_444i), prausnitzii, Ruminococcus prausnitzii, (clade_478 or clade_478i) torques Ruminococcus torques N570.S 3 3 100 100 (clade_360 or clade_360c Dorea longicatena, Dorea longicatena, or clade_360g or Eubacterium rectale, Eubacterium rectale, clade_360h or Faecalibacterium Faecalibacterium clade_360i), (clade_444 prausnitzii prausnitzii or clade_444i), (clade_478 or clade_478i) N579.S 3 3 100 100 (clade_262 or Eubacterium hallii, Eubacterium hallii, clade_262i), clade_396, Eubacterium rectale, Eubacterium rectale, (clade_444 or clade_444i) Ruminococcus torques Ruminococcus torques N602.S 3 3 100 100 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_478 Roseburia inulinivorans, Roseburia inulinivorans, or clade_478i) Subdoligranulum variabile Subdoligranulum variabile N614.S 3 3 100 100 (clade_262 or Clostridium leptum, Clostridium leptum, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_537 prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N648.S 3 3 100 100 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Faecalibacterium Faecalibacterium or clade_360c or prausnitzii, Ruminococcus prausnitzii, clade_360g or clade_360h torques Ruminococcus torques or clade_360i), (clade_478 or clade_478i) N652.S 3 3 100 100 clade_393, (clade_444 or Coprococcus catus, Coprococcus catus, clade_444i), (clade_522 Eubacterium eligens, Eubacterium eligens, or clade_522i) Eubacterium rectale Eubacterium rectale N655.S 2 3 100 100 (clade_444 or Eubactenum rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i) prausnitzii, prausnitzii, Subdoligranulum variabile Subdoligranulum variabile N672.S 3 3 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Pseudoflavonifractor Pseudoflavonifractor or clade_444i), clade_494 capillosus, Ruminococcus capillosus, Ruminococcus torques torques N681.S 2 3 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i) prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N690.S 3 3 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, (clade_444 or clade_444i) Roseburia inulinivorans Roseburia inulinivorans N692.S 3 3 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or hallii Eubacterium hallii clade_360g or clade_360h or clade_360i), clade_396 N698.S 2 3 100 100 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Roseburia intestinalis, Roseburia intestinalis, or clade_478i) Subdoligranulum variabile Subdoligranulum variabile N737.S 3 3 100 100 (clade_262 or Coprococcus catus, Coprococcus catus, clade_262i), clade_393, Eubacterium rectale, Eubacterium rectale, (clade_444 or clade_444i) Ruminococcus torques Ruminococcus torques N738.S 3 3 100 100 (clade_262 or Faecalibacterium Faecalibacterium clade_262i), (clade_478 prausnitzii, Holdemania prausnitzii, Holdemania or clade_478i), clade_485 filiformis, Ruminococcus filiformis, Ruminococcus torques torques N785 3 3 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Eubacterium Dorea longicatena, or clade_360c or ventriosum Eubacterium ventriosum clade_360g or clade_360h or clade_360i), clade_519 N841 3 3 100 100 (clade_262 or Faecalibacterium Faecalibacterium clade_262i), (clade_478 prausnitzii, Ruminococcus prausnitzii, or clade_478i), clade_537 bromii, Ruminococcus Ruminococcus bromii, torques Ruminococcus torques N878 2 3 100 100 (clade_444 or Eubacterium eligens, Eubacterium eligens, clade_444i), (clade_522 Roseburia intestinalis, Roseburia intestinalis, or clade_522i) Roseburia inulinivorans Roseburia inulinivorans N880 2 3 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i) Roseburia inulinivorans Roseburia inulinivorans N881 2 3 100 100 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i) Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans Roseburia inulinivorans N987 3 3 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396, Eubacterium hallii, Eubacterium hallii, clade_537 Ruminococcus bromii Ruminococcus bromii N988 3 3 100 100 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Ruminococcus bromii, Ruminococcus bromii, or clade_478i), clade_537 Subdoligranulum variabile Subdoligranulum variabile N996 3 3 100 100 clade_393, clade_396, Coprococcus catus, Coprococcus catus, (clade_444 or clade_444i) Eubacterium hallii, Eubacterium hallii, Roseburia inulinivorans Roseburia inulinivorans N1061 3 3 100 100 (clade_262 or Eubacterium hallii, Eubacterium hallii, clade_262i), clade_396, Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N479.S 3 3 66.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_500 prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N538.S 3 3 66.7 100 (clade_262 or Desulfovibrio Desulfovibrio clade_262i), clade_445, desulfuricans, desulfuricans, clade_494 Pseudoflavonifractor Pseudoflavonifractor capillosus, Ruminococcus capillosus, Ruminococcus torques torques N542.S 3 3 66.7 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), (clade_444 Eubacterium rectale, Eubacterium rectale, or clade_444i), clade_500 Ruminococcus torques Ruminococcus torques N578.S 3 3 66.7 100 (clade_262 or Desulfovibrio Desulfovibrio clade_262i), clade_445, desulfuricans, desulfuricans, (clade_478 or clade_478i) Faecalibacterium Faecalibacterium prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N609.S 3 3 66.7 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), clade_286, Parabacteroides merdae, Parabacteroides merdae, (clade_444 or clade_444i) Ruminococcus torques Ruminococcus torques N611.S 3 3 66.7 100 (clade_262 or Bacteroides dorei, Bacteroides dorei, clade_262i), (clade_378 Faecalibacterium Faecalibacterium or clade_378e), prausnitzii, Ruminococcus prausnitzii, (clade_478 or clade_478i) torques Ruminococcus torques N617.S 3 3 66.7 100 (clade_262 or Alistipes putredinis, Dorea Alistipes putredinis, clade_262i), (clade_360 longicatena, Dorea longicatena, or clade_360c or Ruminococcus torques Ruminococcus torques clade_360g or clade_360h or clade_360i), clade_500 N666.S 3 3 66.7 100 (clade_444 or Bilophila wadsworthia, Bilophila wadsworthia, clade_444i), clade_521, Eubacterium eligens, Eubacterium eligens, (clade_522 or clade_522i) Eubacterium rectale Eubacterium rectale N675.S 3 3 66.7 100 (clade_262 or Bacteroides ovatus, Bacteroides ovatus, clade_262i), (clade_38 or Faecalibacterium Faecalibacterium clade_38e or clade_38i), prausnitzii, Ruminococcus prausnitzii, (clade_478 or clade_478i) torques Ruminococcus torques N682.S 3 3 66.7 100 clade_170, (clade_444 or Bacteroides caccae, Bacteroides caccae, clade_444i), (clade_478 Eubacterium rectale, Eubacterium rectale, or clade_478i) Faecalibacterium Faecalibacterium prausnitzii prausnitzii N844 3 3 66.7 100 (clade_262 or Bilophila wadsworthia, Bilophila wadsworthia, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena Dorea longicatena clade_360g or clade_360h or clade_360i), clade_521 N845 3 3 66.7 100 (clade_262 or Bacteroides dorei, Bacteroides dorei, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena Dorea longicatena clade_360g or clade_360h or clade_360i), (clade_378 or clade_378e) N846 3 3 66.7 100 clade_170, (clade_262 or Bacteroides caccae, Bacteroides caccae, clade_262i), (clade_360 Coprococcus comes, Dorea Coprococcus comes, or clade_360c or longicatena Dorea longicatena clade_360g or clade_360h clade_360i) N852 3 3 66.7 100 (clade_172 or Bifidobacterium longum, Bifidobacterium longum, clade_172i), (clade_262 Faecalibacterium Faecalibacterium or clade_262i), prausnitzii, Ruminococcus prausnitzii, (clade_478 or clade_478i) torques Ruminococcus torques N876 2 3 66.7 100 clade_170, (clade_444 or Bacteroides caccae, Bacteroides caccae, clade_444i) Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans Roseburia inulinivorans N982 3 3 66.7 100 (clade_172 or Bifidobacterium longum, Bifidobacterium longum, clade_172i), (clade_262 Coprococcus comes, Coprococcus comes, or clade_262i), clade_396 Eubacterium hallii Eubacterium hallii N1008 3 3 66.7 100 (clade_262 or Bilophila wadsworthia, Bilophila wadsworthia, clade_262i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), clade_521 prausnitzii, Ruminococcus prausnitzii, torques Ruminococcus torques N649.S 3 3 33.3 100 (clade_378 or Bacteroides dorei, Bacteroides dorei, clade_378e), (clade_444 Desulfovibrio Desulfovibrio or clade_444i), clade_445 desulfuricans, Eubacterium desulfuricans, rectale Eubacterium rectale N657.S 3 3 33.3 100 (clade_378 or Bacteroides dorei, Bacteroides dorei, clade_378e), (clade_38 or Bacteroides ovatus, Bacteroides ovatus, clade_38e or clade_38i), Faecalibacterium Faecalibacterium (clade_478 or clade_478i) prausnitzii prausnitzii N678.S 3 3 33.3 100 clade_445, (clade_478 or Akkermansia muciniphila, Akkermansia clade_478i), clade_583 Desulfovibrio muciniphila, desulfuricans, Desulfovibrio Faecalibacterium desulfuricans, prausnitzii Faecalibacterium prausnitzii N686.S 3 3 33.3 100 (clade_378 or Bacteroides dorei, Bacteroides dorei, clade_378e), (clade_38 or Bacteroides ovatus, Bacteroides ovatus, clade_38e or clade_38i), Holdemania filiformis Holdemania filiformis clade_485 N710.S 3 3 33.3 100 (clade_478 or Alistipes putredinis, Alistipes putredinis, clade_478i), clade_500, Gordonibacter pamelaeae, Gordonibacter pamelaeae, (clade_566 or clade_566f) Subdoligranulum variabile Subdoligranulum variabile N522.S 3 3 100 66.7 (clade_408 or clade_408b Clostridium symbiosum, Eubacterium siraeum, or clade_408d or Eubacterium siraeum, Pseudoflavonifractor clade_408f or clade_408g Pseudoflavonifractor capillosus or clade_408h), capillosus clade_494, clade_538 N651.S 3 3 100 66.7 (clade_444 or Anaerotruncus Eubacterium eligens, clade_444i), (clade_516 colihominis, Eubacterium Roseburia inulinivorans or clade_516c or eligens, Roseburia clade_516g or inulinivorans clade_516h), (clade_522 or clade_522i) N653.S 3 3 100 66.7 clade_396, (clade_408 or Anaerostipes caccae, Eubacterium ballii, clade_408b or clade_408d Eubacterium hallii, Eubacterium rectale or clade_408f or Eubacterium rectale clade_408g or clade_408h), (clade_444 or clade_444i) N654.S 3 3 100 66.7 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), prausnitzii, Ruminococcus prausnitzii (clade_516 or clade_516c albus or clade_516g or clade_516h) N680.S 3 3 100 66.7 (clade_262 or Blautia hydrogenotrophica, Faecalibacterium clade_262i), clade_368, Faecalibacterium prausnitzii, (clade_478 or clade_478i) prausnitzii, Ruminococcus Ruminococcus torques torques N712.S 2 3 100 66.7 (clade_260 or clade_260c Clostridium scindens, Faecalibacterium or clade_260g or Faecalibacterium prausnitzii, clade_260h), (clade_478 prausnitzii, Subdoligranulum or clade_478i) Subdoligranulum variabile variabile N792 3 3 100 66.7 (clade_444 or Clostridium Eubacterium rectale, clade_444i), (clade_478 methylpentosum, Subdoligranulum or clade_478i), Eubacterium rectale, variabile (clade_516 or clade_516c Subdoligranulum variabile or clade_516g or clade_516h) N802 3 3 100 66.7 (clade_408 or clade_408b Anaerostipes caccae, Clostridium leptum, or clade_408d or Clostridium leptum, Holdemania filiformis clade_408f or clade_408g Holdemania filiformis or clade_408h), clade_485, clade_537 N804 3 3 100 66.7 clade_485, clade_494, Coprococcus eutactus, Holdemania filiformis, clade_543 Holdemania filiformis, Pseudoflavonifractor Pseudoflavonifractor capillosus capillosus N807 3 3 100 66.7 (clade_262 or Anaerostipes caccae, Coprococcus comes, clade_262i), (clade_408 Coprococcus comes, Subdoligranulum or clade_408b or Subdoligranulum variabile variabile clade_408d or clade_408f or clade_408g or clade_408h), (clade_478 or clade_478i) N849 3 3 100 66.7 (clade_444 or Clostridium cocleatum, Eubacterium eligens, clade_444i), (clade_481 Eubacterium eligens, Eubacterium rectale or clade_481a or Eubacterium rectale clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_522 or clade_522i) N858 3 3 100 66.7 (clade_262 or Anaerostipes caccae, Pseudoflavonifractor clade_262i), (clade_408 Pseudoflavonifractor capillosus, Ruminococcus or clade_408b or capillosus, Ruminococcus torques clade_408d or clade_408f torques or clade_408g or clade_408h), clade_494 N859 3 3 100 66.7 (clade_260 or clade_260c Clostridium scindens, Pseudoflavonifractor or clade_260g or Pseudoflavonifractor capillosus, Ruminococcus clade_260h), (clade_262 capillosus, Ruminococcus torques or clade_262i), clade_494 torques N875 2 3 100 66.7 (clade_444 or Anaerotruncus Roseburia intestinalis, clade_444i), (clade_516 colihominis, Roseburia Roseburia inulinivorans or clade_516c or intestinalis, Roseburia clade_516g or inulinivorans clade_516h) N885 3 3 100 66.7 (clade_408 or clade_408b Anaerostipes caccae, Faecalibacterium or clade_408d or Faecalibacterium prausnitzii, Holdemania clade_408f or clade_408g prausnitzii, Holdemania filiformis or clade_408h), filiformis (clade_478 or clade_478i), clade_485 N942 3 3 100 66.7 (clade_260 or clade_260c Clostridium scindens, Eubacterium ball, or clade_260g or Eubacterium hallii, Roseburia inulinivorans clade_260h), clade_396, Roseburia inulinivorans (clade_444 or clade_444i) N961 3 3 100 66.7 (clade_354 or Clostridium bartlettii, Eubacterium rectale, clade_354e), (clade_444 Eubacterium rectale, Subdoligranulum or clade_444i), Subdoligranulum variabile variabile (clade_478 or clade_478i) N972 3 3 100 66.7 (clade_444 or Anaerotruncus Eubacterium rectale, clade_444i), (clade_478 colihominis, Eubacterium Subdoligranulum or clade_478i), rectale, Subdoligranulum variabile (clade_516 or clade_516c variabile or clade_516g or clade_516h) N1051 3 3 100 66.7 (clade_262 or Anaerotruncus Faecalibacterium clade_262i), (clade_478 colihominis, prausnitzii, or clade_478i), Faecalibacterium Ruminococcus torques (clade_516 or clade_516c prausnitzii, Ruminococcus or clade_516g or torques clade_516h) N587.S 3 3 66.7 66.7 (clade_478 or Alistipes putredinis, Alistipes putredinis, clade_478i), clade_500, Clostridium Subdoligranulum (clade_516 or clade_516c methylpentosum, variabile or clade_516g or Subdoligranulum variabile clade_516h) N589.S 3 3 66.7 66.7 (clade_262 or Bifidobacterium bifidum, Faecalibacterium clade_262i), clade_293, Faecalibacterium prausnitzii, (clade_478 or clade_478i) prausnitzii, Ruminococcus Ruminococcus torques torques N612.S 3 3 66.7 66.7 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Ruminococcus torques, Ruminococcus torques or clade_444i), (clade_98 Streptococcus salivarius or clade_98i) N625.S 3 3 66.7 66.7 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i), (clade_98 prausnitzii, Streptococcus prausnitzii or clade_98i) salivarius N656.S 3 3 66.7 66.7 clade_170, clade_396, Bacteroides caccae, Bacteroides caccae, clade_537 Bacteroides pectinophilus, Clostridium leptum Clostridium leptum N714.S 2 3 66.7 66.7 (clade_478 or Faecalibacterium Faecalibacterium clade_478i), (clade_98 or prausnitzii, Streptococcus prausnitzii, clade_98i) thermophilus, Subdoligranulum Subdoligranulum variabile variabile N779 3 3 66.7 66.7 (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i), (clade_98 intestinalis, Streptococcus intestinalis or clade_98i) australis N781 3 3 66.7 66.7 clade_293, clade_393, Bifidobacterium bifidum, Coprococcus catus, (clade_444 or clade_444i) Coprococcus catus, Eubacterium rectale Eubacterium rectale N828 3 3 66.7 66.7 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena, Streptococcus Dorea longicatena or clade_360c or australis clade_360g or clade_360h or clade_360i), (clade_98 or clade_98i) N829 3 3 66.7 66.7 (clade_262 or Bacteroides fragilis, Coprococcus comes, clade_262i), (clade_360 Coprococcus comes, Dorea Dorea longicatena or clade_360c or longicatena clade_360g or clade_360h or clade_360i), (clade_65 or clade_65e) N860 3 3 66.7 66.7 (clade_262 or Pseudoflavonifractor Pseudoflavonifractor clade_262i), clade_494, capillosus, Ruminococcus capillosus, Ruminococcus (clade_98 or clade_98i) torques, Streptococcus torques thermophilus N894 3 3 66.7 66.7 clade_293, (clade_444 or Bifidobacterium bifidum, Eubacterium rectale, clade_444i), (clade_478 Eubacterium rectale, Subdoligranulum or clade_478i) Subdoligranulum variabile variabile N925 3 3 66.7 66.7 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_98 or Roseburia inulinivorans, Roseburia inulinivorans clade_98i) Streptococcus australis N927 3 3 66.7 66.7 clade_396, (clade_444 or Dialister invisus, Eubacterium hallii, clade_444i), clade_506 Eubacterium hallii, Roseburia inulinivorans Roseburia inulinivorans N935 3 3 66.7 66.7 clade_396, (clade_444 or Bacteroides fragilis, Eubacterium hallii, clade_444i), (clade_65 or Eubacterium hallii, Roseburia inulinivorans clade_65e) Roseburia inulinivorans N947 3 3 66.7 66.7 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_98 or Roseburia inulinivorans, Roseburia inulinivorans clade_98i) Streptococcus thermophilus N983 3 3 66.7 66.7 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i), (clade_98 or Roseburia inulinivorans, Roseburia inulinivorans clade_98i) Streptococcus salivarius N1023 3 3 66.7 66.7 (clade_262 or Dorea longicatena, Dorea longicatena, clade_262i), (clade_360 Ruminococcus torques, Ruminococcus torques or clade_360c or Streptococcus salivarius clade_360g or clade_360h or clade_360i), (clade_98 or clade_98i) N441.S 3 3 100 33.3 clade_252, (clade_262 or Clostridium butyricum, Ruminococcus torques clade_262i), (clade_354 Eubacterium tenue, or clade_354e) Ruminococcus torques N584.S 3 3 100 33.3 (clade_262 or Clostridium symbiosum, Coprococcus comes clade_262i), (clade_408 Collinsella aerofaciens, or clade_408b or Coprococcus comes clade_408d or clade_408f or clade_408g or clade_408h), (clade_553 or clade_553i) N794 3 3 100 33.3 (clade_516 or clade_516c Anaerotruncus Clostridium leptum or clade_516g or colihominis, Clostridium clade_516h), clade_537, leptum, Coprococcus clade_543 eutactus N788 1 3 100 0 (clade_516 or clade_516c Anaerotruncus or clade_516g or colihominis, Clostridium clade_516h) methylpentosum, Ruminococcus albus N524.S 1 2 100 100 (clade_478 or clade_478i) Faecalibacterium Faecalibacterium prausnitzii, prausnitzii, Subdoligranulum variabile Subdoligranulum variabile N604.S 2 2 100 100 (clade_262 or Faecalibacterium Faecalibacterium clade_262i), (clade_478 prausnitzii, Ruminococcus prausnitzii, or clade_478i) torques Ruminococcus torques N610.S 2 2 100 100 (clade_262 or Eubacterium rectale, Eubacterium rectale, clade_262i), (clade_444 Ruminococcus torques Ruminococcus torques or clade_444i) N623.S 2 2 100 100 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Faecalibacterium Faecalibacterium or clade_478i) prausnitzii prausnitzii N663.S 2 2 100 100 (clade_360 or clade_360c Dorea longicatena, Dorea longicatena, or clade_360g or Roseburia inulinivorans Roseburia inulinivorans clade_360h or clade_360i), (clade_444 or clade_444i) N669.S 2 2 100 100 (clade_262 or Coprococcus comes, Dorea Coprococcus comes, clade_262i), (clade_360 longicatena Dorea longicatena or clade_360c or clade_360g or clade_360h clade_360i) N676.S 2 2 100 100 (clade_262 or Pseudoflavonifractor Pseudoflavonifractor clade_262i), clade_494 capillosus, Ruminococcus capillosus, Ruminococcus torques torques N703.S 2 2 100 100 (clade_478 or Faecalibacterium Faecalibacterium clade_478i), clade_485 prausnitzii, Holdemania prausnitzii, Holdemania filiformis filiformis N775.S 2 2 100 100 (clade_262 or Coprococcus comes, Coprococcus comes, clade_262i), clade_396 Eubacterium hallii Eubacterium hallii N777.S 2 2 100 100 (clade_444 or Eubacterium ventriosum, Eubacterium ventriosum, clade_444i), clade_519 Roseburia inulinivorans Roseburia inulinivorans N780.S 2 2 100 100 (clade_444 or Faecalibacterium Faecalibacterium clade_444i), (clade_478 prausnitzii, Roseburia prausnitzii, Roseburia or clade_478i) intestinalis intestinalis N817.S 2 2 100 100 clade_519, clade_537 Clostridium leptum, Clostridium leptum, Eubacterium ventriosum Eubacterium ventriosum N827.S 2 2 100 100 (clade_444 or Eubacterium eligens, Eubacterium eligens, clade_444i), (clade_522 Eubacterium rectale Eubacterium rectale or clade_522i) N836.S 2 2 100 100 (clade_478 or Pseudoflavonifractor Pseudoflavonifractor clade_478i), clade_494 capillosus, capillosus, Subdoligranulum variabile Subdoligranulum variabile N871.S 1 2 100 100 (clade_444 or clade_444i) Roseburia intestinalis, Roseburia intestinalis, Roseburia inulinivorans Roseburia inulinivorans N874.S 2 2 100 100 clade_396, (clade_444 or Eubacterium hallii, Eubacterium hallii, clade_444i) Roseburia inulinivorans Roseburia inulinivorans N898.S 2 2 100 100 (clade_444 or Eubacterium rectale, Eubacterium rectale, clade_444i), (clade_478 Subdoligranulum variabile Subdoligranulum or clade_478i) variabile N907.S 2 2 100 100 (clade_360 or clade_360c Dorea longicatena, Dorea longicatena, or clade_360g or Roseburia intestinalis Roseburia intestinalis clade_360h or clade_360i), (clade_444 or clade_444i) N998.S 2 2 100 100 clade_393, (clade_478 or Coprococcus catus, Coprococcus catus, clade_478i) Faecalibacterium Faecalibacterium prausnitzii prausnitzii N1088 2 2 100 100 clade_393, (clade_444 or Coprococcus catus, Coprococcus catus, clade_444i) Eubacterium rectale Eubacterium rectale N1089 2 2 100 100 (clade_478 or Clostridium Clostridium clade_478i), clade_576 lactatifermentans, lactatifermentans, Faecalibacterium Faecalibacterium prausnitzii prausnitzii N660.S 2 2 50 100 (clade_172 or Bifidobacterium longum, Bifidobacterium longum, clade_172i), clade_485 Holdemania filiformis Holdemania filiformis N665.S 2 2 50 100 clade_286, (clade_444 or Parabacteroides merdae, Parabacteroides merdae, clade_444i) Roseburia intestinalis Roseburia intestinalis N667.S 2 2 50 100 clade_500, (clade_522 or Alistipes putredinis, Alistipes putredinis, clade_522i) Eubacterium eligens Eubacterium eligens N733.S 2 2 50 100 (clade_262 or Bacteroides ovatus, Bacteroides ovatus, clade_262i), (clade_38 or Ruminococcus torques Ruminococcus torques clade_38e or clade_38i) N734.S 2 2 50 100 (clade_262 or Bilophila wadsworthia, Bilophila wadsworthia, clade_262i), clade_521 Ruminococcus torques Ruminococcus torques N739.S 2 2 50 100 (clade_478 or Alistipes putredinis, Alistipes putredinis, clade_478i), clade_500 Faecalibacterium Faecalibacterium prausnitzii prausnitzii N741.S 2 2 50 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_500 Ruminococcus torques Ruminococcus torques N782.S 2 2 50 100 clade_171, (clade_522 or Bacteroides intestinalis, Bacteroides intestinalis, clade_522i) Eubacterium eligens Eubacterium eligens N789.S 2 2 50 100 clade_357, clade_537 Clostridium leptum, Clostridium leptum, Oxalobacter formigenes Oxalobacter formigenes N796.S 2 2 50 100 clade_500, clade_537 Alistipes putredinis, Alistipes putredinis, Ruminococcus bromii Ruminococcus bromii N798.S 2 2 50 100 (clade_378 or Bacteroides dorei, Bacteroides dorei, clade_378e), clade_494 Pseudoflavonifractor Pseudoflavonifractor capillosus capillosus N800.S 2 2 50 100 clade_445, clade_537 Clostridium leptum, Clostridium leptum, Desulfovibrio Desulfovibrio desulfuricans desulfuricans N809.S 2 2 50 100 clade_445, (clade_478 or Desulfovibrio Desulfovibrio clade_478i) desulfuricans, desulfuricans, Faecalibacterium Faecalibacterium prausnitzii prausnitzii N816.S 2 2 50 100 (clade_38 or clade_38e or Bacteroides ovatus, Bacteroides ovatus, clade_38i), (clade_522 or Eubacterium eligens Eubacterium eligens clade_522i) N842.S 2 2 50 100 clade_393, clade_500 Alistipes putredinis, Alistipes putredinis, Coprococcus catus Coprococcus catus N843.S 2 2 50 100 (clade_262 or Alistipes putredinis, Alistipes putredinis, clade_262i), clade_500 Coprococcus comes Coprococcus comes N869.S 2 2 50 100 clade_537, (clade_566 or Clostridium leptum, Clostridium leptum, clade_566f) Gordonibacter pamelaeae Gordonibacter pamelaeae N986.S 2 2 50 100 (clade_172 or Bifidobacterium longum, Bifidobacterium longum, clade_172i), (clade_262 Ruminococcus torques Ruminococcus torques or clade_262i) N995.S 2 2 50 100 clade_500, clade_537 Alistipes putredinis, Alistipes putredinis, Clostridium leptum Clostridium leptum N1002.S 2 2 50 100 (clade_478 or Alistipes putredinis, Alistipes putredinis, clade_478i), clade_500 Subdoligranulum variabile Subdoligranulum variabile N1004.S 2 2 50 100 (clade_262 or Desulfovibrio Desulfovibrio clade_262i), clade_445 desulfuricans, desulfuricans, Ruminococcus torques Ruminococcus torques N1019.S 2 2 50 100 clade_358, (clade_478 or Faecalibacterium Faecalibacterium clade_478i) prausnitzii, Veillonella prausnitzii, Veillonella atypica atypica N1093 2 2 50 100 (clade_522 or Akkermansia muciniphila, Akkermansia clade_522i), clade_583 Eubacterium eligens muciniphila, Eubacterium eligens N668.S 2 2 0 100 (clade_378 or Alistipes putredinis, Alistipes putredinis, clade_378e), clade_500 Bacteroides dorei Bacteroides dorei N685.S 2 2 0 100 clade_170, clade_286 Bacteroides caccae, Bacteroides caccae, Parabacteroides merdae Parabacteroides merdae N835.S 2 2 0 100 clade_500, (clade_566 or Alistipes putredinis, Alistipes putredinis, clade_566f) Gordonibacter pamelaeae Gordonibacter pamelaeae N851.S 2 2 0 100 clade_445, clade_521 Bilophila wadsworthia, Bilophila wadsworthia, Desulfovibrio Desulfovibrio desulfuricans desulfuricans N464.S 2 2 100 50 clade_252, (clade_262 or Clostridium butyricum, Ruminococcus torques clade_262i) Ruminococcus torques N695.S 2 2 100 50 clade_396, (clade_516 or Eubacterium hallii, Eubacterium hallii clade_516c or clade_516g Ruminococcus albus or clade_516h) N776.S 2 2 100 50 (clade_516 or clade_516c Eubacterium siraeum, Eubacterium siraeum or clade_516g or Ruminococcus albus clade_516h), clade_538 N793.S 2 2 100 50 (clade_516 or clade_516c Anaerotruncus Clostridium leptum or clade_516g or colihominis, Clostridium clade_516h), clade_537 leptum N815.S 2 2 100 50 (clade_522 or Collinsella aerofaciens, Eubacterium eligens clade_522i), (clade_553 Eubacterium eligens or clade_553i) N833.S 2 2 100 50 (clade_260 or clade_260c Clostridium scindens, Coprococcus comes or clade_260g or Coprococcus comes clade_260h), (clade_262 or clade_262i) N891.S 2 2 100 50 clade_368, clade_485 Blautia hydrogenotrophica, Holdemania filiformis Holdemania filiformis N1070.S 2 2 100 50 (clade_262 or Anaerotruncus Coprococcus comes clade_262i), (clade_516 colihominis, Coprococcus or clade_516c or comes clade_516g or clade_516h) N1092 2 2 100 50 clade_393, (clade_481 or Clostridium cocleatum, Coprococcus catus clade_481a or clade_481b Coprococcus catus or clade_481e or clade_481g or clade_481h or clade_481i) N795.S 2 2 50 50 clade_500, (clade_516 or Alistipes putredinis, Alistipes putredinis clade_516c or clade_516g Clostridium or clade_516h) methylpentosum N797.S 2 2 50 50 (clade_478 or Faecalibacterium Faecalibacterium clade_478i), (clade_98 or prausnitzii, Streptococcus prausnitzii clade_98i) salivarius N808.S 2 2 50 50 clade_445, (clade_516 or Clostridium Desulfovibrio clade_516c or clade_516g methylpentosum, desulfuricans or clade_516h) Desulfovibrio desulfuricans N811.S 2 2 50 50 clade_445, (clade_516 or Desulfovibrio Desulfovibrio clade_516c or clade_516g desulfuricans, desulfuricans or clade_516h) Ruminococcus albus N826.S 2 2 50 50 clade_500, clade_543 Alistipes putredinis, Alistipes putredinis Coprococcus eutactus N830.S 2 2 50 50 (clade_262 or Coprococcus comes, Coprococcus comes clade_262i), (clade_98 or Streptococcus clade_98i) thermophilus N832.S 2 2 50 50 clade_293, (clade_478 or Bifidobacterium bifidum, Subdoligranulum clade_478i) Subdoligranulum variabile variabile N840.S 2 2 50 50 (clade_444 or Eubacterium rectale, Eubacterium rectale clade_444i), (clade_98 or Streptococcus salivarius clade_98i) N945.S 2 2 50 50 (clade_260 or clade_260c Alistipes putredinis, Alistipes putredinis or clade_260g or Clostridium scindens clade_260h), clade_500 N960.S 2 2 50 50 (clade_354 or Alistipes putredinis, Alistipes putredinis clade_354e), clade_500 Clostridium bartlettii N968.S 2 2 50 50 (clade_262 or Escherichia coli, Ruminococcus torques clade_262i), (clade_92 or Ruminococcus torques clade_92e or clade_92i) N1091 2 2 50 50 (clade_444 or Alistipes indistinctus, Eubacterium rectale clade_444i), clade_561 Eubacterium rectale N805.S 2 2 0 50 clade_293, clade_445 Bifidobacterium bifidum, Desulfovibrio Desulfovibrio desulfuricans desulfuricans N822.S 2 2 0 50 clade_401, clade_500 Alistipes putredinis, Alistipes putredinis Lactococcus lactis N928.S 2 2 0 50 clade_500, clade_506 Alistipes putredinis, Alistipes putredinis Dialister invisus N936.S 2 2 0 50 clade_500, (clade_65 or Alistipes putredinis, Alistipes putredinis clade_65e) Bacteroides fragilis N1078.S 2 2 0 50 clade_445, (clade_98 or Desulfovibrio Desulfovibrio clade_98i) desulfuricans, desulfuricans Streptococcus australis N913.S 2 2 100 0 (clade_408 or clade_408b Anaerotruncus or clade_408d or colihominis, Clostridium clade_408f or clade_408g symbiosum or clade_408h), (clade_516 or clade_516c or clade_516g or clade_516h)

Network Ecologies comprised of one or more clades, or two or more OTUs that are observed in the ethanol-treated spore preparation or the combined engrafted and augmented ecologies of at least one patient post-treatment with the bacterial composition. Network Ecologies are defined based on their clade or OTU content. The respective clades and 16S genetic sequences for each OTU are defined in Table 1. Network Ecology IDs with a “.s” indicates that the network is a subset of the computationally determined networks reported in Table 8 with the same Network Ecology ID.

TABLE 14B Percent of Percent of Combined Combined Augmented & Augmented & Percent of Engrafted Percent of Engrafted Ethanol- Post- Ethanol- Post- treated Treatment treated Treatment spore Patient spore Patient Network Number Preparations Ecologies Number Preparations Ecologies Ecology of Containing Containing of Containing Containing ID OTUs Network Network Clades Network Network N262.S 15 0 0 10 0 10 N290.S 14 0 0 10 20 10 N271.S 13 0 0 9 0 10 N282.S 13 0 0 9 0 10 N284.S 13 0 0 9 0 10 N302.S 12 0 0 8 20 10 N279.S 12 0 0 9 0 10 N288.S 12 0 0 8 0 10 N310.S 11 0 0 7 20 10 N323.S 11 0 0 7 20 10 N331.S 11 0 0 7 0 10 N332.S 11 0 0 8 0 10 N312.S 10 0 0 7 20 10 N325.S 10 0 0 8 20 10 N338.S 10 0 0 7 20 10 N339.S 10 0 0 7 20 10 N340.S 10 0 0 7 20 10 N341.S 10 0 0 7 20 10 N301.S 10 0 0 7 0 10 N346.S 10 0 0 7 0 10 N381.S 9 0 10 7 70 70 N343.S 9 10 0 7 20 0 N336.S 9 0 0 6 20 10 N353.S 9 0 0 7 20 0 N355.S 9 0 0 6 20 10 N356.S 9 0 0 6 20 10 N361.S 9 0 0 6 20 10 N329.S 9 0 0 6 10 0 N345.S 9 0 0 7 0 10 N344.S 8 10 0 6 20 10 N374.S 8 10 0 6 20 10 N375.S 8 10 0 6 20 10 N352.S 8 0 0 5 20 10 N358.S 8 0 0 5 20 10 N368.S 8 0 0 6 20 10 N369.S 8 0 0 6 20 10 N372.S 8 0 0 6 20 10 N377.S 8 0 0 6 20 0 N380.S 8 0 10 7 10 10 N357.S 8 0 0 6 0 10 N370.S 7 10 0 5 20 10 N389.S 7 10 0 6 20 10 N390.S 7 10 0 6 20 0 N394.S 7 10 0 5 20 10 N396.S 7 10 0 6 20 0 N376.S 7 0 0 5 20 10 N431.S 7 0 10 6 10 10 N434.S 7 0 10 6 10 10 N387.S 7 10 0 6 10 0 N397.S 7 0 0 6 10 0 N440.S 7 0 0 7 10 0 N373.S 7 0 0 6 0 10 N403.S 6 0 50 4 100 80 N432.S 6 0 50 4 100 70 N399.S 6 60 30 6 100 80 N493.S 6 50 30 6 100 70 N436.S 6 20 30 4 100 80 N437.S 6 20 30 3 100 80 N490.S 6 0 0 5 100 40 N414.S 6 40 50 5 70 80 N457.S 6 0 40 5 70 80 N430.S 6 30 40 6 60 50 N402.S 6 50 20 5 60 20 N447.S 6 20 10 5 50 20 N439.S 6 20 0 6 50 0 N415.S 6 20 10 5 30 10 N422.S 6 0 10 5 20 10 N421.S 6 20 0 6 20 10 N386.S 6 10 0 5 20 10 N416.S 6 0 0 6 20 10 N458.S 6 0 10 6 10 10 N459.S 6 0 10 5 10 10 N405.S 6 0 0 4 10 0 N526 6 0 0 5 10 0 N423.S 6 0 10 5 0 10 N545 6 0 0 5 0 10 N433.S 5 90 60 4 100 80 N508.S 5 0 50 4 100 80 N511.S 5 0 50 3 100 80 N488.S 5 0 40 4 100 80 N518.S 5 50 30 5 100 70 N448.S 5 30 30 4 100 80 N474.S 5 40 10 5 100 60 N520.S 5 20 10 5 100 50 N509.S 5 70 50 5 80 50 N510.S 5 40 50 5 70 80 N519.S 5 40 30 5 60 30 N429.S 5 0 30 4 60 50 N463.S 5 0 30 5 50 50 N382.S 5 20 0 5 50 0 N514.S 5 20 0 5 50 10 N450.S 5 0 10 5 20 10 N477.S 5 0 10 5 20 10 N535.S 5 0 10 4 20 30 N446.S 5 20 0 5 20 10 N468.S 5 20 0 5 20 0 N451.S 5 10 0 4 20 10 N408.S 5 0 0 5 20 10 N419.S 5 0 0 5 20 10 N465.S 5 0 0 4 20 0 N586 5 0 0 3 20 0 N516.S 5 10 0 5 10 0 N521.S 5 10 0 5 10 0 N537.S 5 10 0 5 10 0 N512.S 4 90 70 3 100 80 N460.S 4 90 60 3 100 80 N517.S 4 90 60 4 100 80 N400.S 4 60 60 4 100 80 N577.S 4 60 60 3 100 70 N582.S 4 50 60 4 100 80 N462.S 4 100 50 3 100 80 N547.S 4 90 50 3 100 80 N548.S 4 70 50 4 100 80 N543.S 4 60 50 4 100 70 N523.S 4 0 50 3 100 80 N616.S 4 90 40 4 100 80 N769 4 40 40 4 100 70 N585.S 4 0 30 2 100 90 N689 4 10 20 4 100 70 N687 4 0 20 4 100 90 N621.S 4 40 10 4 100 90 N574.S 4 60 0 4 100 50 N709 4 30 0 4 100 60 N580.S 4 20 0 4 100 40 N664 4 20 10 4 70 10 N515.S 4 40 0 4 70 0 N597.S 4 0 0 3 70 50 N591.S 4 40 30 4 60 30 N730 4 30 10 4 60 20 N693 4 10 10 4 60 30 N534.S 4 30 40 4 40 40 N590.S 4 30 30 3 30 30 N466.S 4 0 10 4 20 10 N480.S 4 0 10 4 20 10 N469.S 4 20 0 4 20 10 N478.S 4 10 0 4 20 0 N484.S 4 10 0 4 20 10 N482.S 4 0 0 4 20 10 N530.S 4 0 0 4 20 10 N481.S 4 10 0 4 10 0 N533.S 4 10 0 4 10 0 N572.S 4 10 0 4 10 0 N525.S 4 0 0 4 10 0 N528.S 4 0 0 4 10 0 N581.S 4 0 10 4 0 10 N737.S 3 90 70 3 100 80 N672.S 3 70 70 3 100 80 N570.S 3 100 60 3 100 90 N655.S 3 100 60 2 100 90 N546.S 3 90 60 3 100 80 N648.S 3 90 60 3 100 80 N681.S 3 90 60 2 100 80 N961 3 90 60 3 100 80 N579.S 3 80 60 3 100 80 N614.S 3 60 60 3 100 70 N539.S 3 0 60 2 100 80 N698.S 3 0 60 2 100 90 N692.S 3 90 50 3 100 80 N529.S 3 70 50 3 100 80 N859 3 40 50 3 100 70 N1061 3 80 40 3 100 80 N841 3 60 40 3 100 70 N988 3 60 40 3 100 80 N858 3 50 40 3 100 80 N602.S 3 30 40 3 100 90 N792 3 20 40 3 100 70 N1051 3 0 40 3 100 70 N881 3 0 40 2 100 90 N972 3 0 40 3 100 70 N712.S 3 60 30 2 100 80 N807 3 50 30 3 100 80 N653.S 3 40 30 3 100 90 N690.S 3 30 30 3 100 80 N880 3 30 30 2 100 80 N996 3 30 30 3 100 90 N714.S 3 100 20 2 100 50 N987 3 50 20 3 100 70 N942 3 20 20 3 100 80 N875 3 0 20 2 100 70 N860 3 70 10 3 100 40 N1023 3 0 10 3 100 40 N612.S 3 0 10 3 100 40 N625.S 3 0 10 3 100 50 N794 3 0 10 3 100 70 N844 3 100 0 3 100 0 N1008 3 90 0 3 100 0 N947 3 30 0 3 100 50 N654.S 3 20 0 3 100 70 N828 3 20 0 3 100 40 N982 3 20 0 3 100 50 N852 3 10 0 3 100 50 N779 3 0 0 3 100 50 N788 3 0 0 1 100 80 N925 3 0 0 3 100 50 N983 3 0 0 3 100 50 N785 3 80 50 3 80 50 N845 3 80 20 3 80 30 N611.S 3 70 20 3 80 30 N652.S 3 40 60 3 70 90 N878 3 0 40 2 70 90 N849 3 20 20 3 70 90 N651.S 3 0 20 3 70 70 N666.S 3 40 0 3 70 0 N441.S 3 10 0 3 70 50 N609.S 3 50 20 3 60 20 N781 3 50 0 3 50 0 N894 3 50 0 3 50 0 N589.S 3 40 0 3 50 0 N584.S 3 30 0 3 50 10 N927 3 30 0 3 50 20 N738.S 3 40 60 3 40 70 N470.S 3 40 50 2 40 70 N829 3 40 40 3 40 40 N802 3 30 30 3 40 70 N885 3 30 20 3 40 70 N804 3 20 20 3 40 70 N935 3 20 20 3 40 40 N656.S 3 30 10 3 30 10 N682.S 3 30 10 3 30 10 N846 3 30 10 3 30 10 N876 3 0 10 2 30 10 N710.S 3 20 10 3 20 10 N479.S 3 10 10 3 20 10 N542.S 3 10 10 3 20 10 N587.S 3 10 10 3 20 10 N617.S 3 10 10 3 20 10 N680.S 3 20 0 3 20 0 N657.S 3 10 10 3 10 10 N675.S 3 0 10 3 10 10 N538.S 3 10 0 3 10 0 N578.S 3 10 0 3 10 0 N649.S 3 10 0 3 10 0 N678.S 3 10 0 3 10 0 N522.S 3 0 10 3 0 10 N686.S 3 0 10 3 0 10 N1088 2 100 80 2 100 90 N898.S 2 100 80 2 100 90 N610.S 2 90 80 2 100 80 N623.S 2 100 70 2 100 90 N669.S 2 100 70 2 100 80 N998.S 2 100 70 2 100 90 N836.S 2 80 70 2 100 90 N676.S 2 70 70 2 100 80 N524.S 2 100 60 1 100 90 N604.S 2 90 60 2 100 80 N793.S 2 0 60 2 100 80 N775.S 2 90 50 2 100 80 N780.S 2 0 50 2 100 90 N907.S 2 0 50 2 100 90 N913.S 2 0 50 2 100 80 N833.S 2 60 40 2 100 70 N874.S 2 30 40 2 100 90 N1070.S 2 0 40 2 100 70 N871.S 2 0 40 1 100 90 N663.S 2 30 30 2 100 90 N1092 2 80 20 2 100 90 N830.S 2 100 10 2 100 40 N869.S 2 50 10 2 100 50 N797.S 2 0 10 2 100 50 N840.S 2 0 10 2 100 50 N734.S 2 90 0 2 100 0 N695.S 2 20 0 2 100 70 N986.S 2 10 0 2 100 50 N817.S 2 60 60 2 80 60 N798.S 2 60 30 2 80 40 N777.S 2 20 30 2 80 50 N968.S 2 70 0 2 80 30 N827.S 2 40 70 2 70 90 N464.S 2 40 40 2 70 50 N665.S 2 0 10 2 60 20 N1089 2 20 60 2 50 60 N832.S 2 50 0 2 50 0 N703.S 2 40 60 2 40 70 N1093 2 40 30 2 40 30 N660.S 2 0 0 2 40 50 N815.S 2 10 0 2 30 10 N1019.S 2 0 30 2 20 30 N1002.S 2 20 10 2 20 10 N685.S 2 20 10 2 20 10 N739.S 2 20 10 2 20 10 N835.S 2 20 10 2 20 10 N842.S 2 20 10 2 20 10 N843.S 2 20 10 2 20 10 N960.S 2 20 10 2 20 10 N995.S 2 20 10 2 20 10 N741.S 2 10 10 2 20 10 N795.S 2 10 10 2 20 10 N945.S 2 10 10 2 20 10 N796.S 2 0 10 2 20 10 N668.S 2 20 0 2 20 0 N891.S 2 20 0 2 20 0 N928.S 2 20 0 2 20 0 N936.S 2 20 0 2 20 0 N667.S 2 0 0 2 20 10 N826.S 2 0 0 2 20 10 N822.S 2 10 10 2 10 10 N733.S 2 0 10 2 10 10 N816.S 2 0 10 2 10 10 N1004.S 2 10 0 2 10 0 N805.S 2 10 0 2 10 0 N809.S 2 10 0 2 10 0 N851.S 2 10 0 2 10 0 N1078.S 2 0 0 2 10 0 N789.S 2 0 0 2 10 0 N800.S 2 0 0 2 10 0 N808.S 2 0 0 2 10 0 N811.S 2 0 0 2 10 0 N1091 2 0 10 2 0 10 N782.S 2 0 10 2 0 10 N776.S 2 0 0 2 0 10

Percentage of clinical ethanol-treated spore preparations, or combined engrafted and augmented ecologies of patient's post-treatment with the bacterial composition in which the Network Ecology is observed. Network Ecologies found in doses and patients post treatment comprised 2-15 OTUs. Network Ecology IDs with a “.s” indicates that the network is a subset of the computationally determined networks reported in Table 8 with the same Network Ecology.

TABLE 15 Percent of EtOH Purified Percent of Percent of Spore Percent of Augmented Engrafted Treatment Pretreatment Keystone Ecologies Ecologies with Ecologies Ecologies with clade with clade clade with clade clade clade_65 20 20 40 20 clade_85 0 0 0 0 clade_98 40 30 100 80 clade_110 10 0 10 0 clade_170 10 0 30 0 clade_172 10 50 100 30 clade_262 50 80 100 30 clade_262 50 80 100 30 clade_286 0 20 60 20 clade_286 0 20 60 20 clade_309 40 100 100 40 clade_358 40 0 20 80 clade_360 20 100 100 60 clade_360 20 100 100 60 clade_378 10 30 80 0 clade_393 10 90 100 10 clade_396 70 90 100 10 clade_408 60 100 100 50 clade_444 70 90 100 10 clade_466 10 0 0 0 clade_478 0 90 100 30 clade_485 60 10 40 10 clade_494 50 80 100 30 clade_500 10 0 20 10 clade_521 0 0 100 30 clade_537 50 90 100 20 clade_538 10 0 0 0 clade_540 90 10 30 10 clade_543 10 90 100 0 clade_572 30 80 100 20 clade_576 50 30 50 30 clade_583 20 10 60 50

Presence of Keystone OTU Clades in ethanol-treated spore population treatment and patient's pretreatment, augmented and engrafted microbial ecologies post-treatment.

TABLE 16 Target Dose Cumulative Mean Mean Max. SP SP (CFU/OTU/ Mortality Min. Rel. Clin. Score Expt. Arm Test Article mouse) (%) Weight (Death = 4) SP-327 3 Vehicle Control 30 0.89 2.2 SP-327 4 Vanco. Positive Control 0 0.99 1 SP-327 12 N1957 2.0E+07 0 0.87 0 SP-327 13 N1957 2.0E+06 40 0.86 2.2 SP-327 14 N1957 2.0E+05 50 0.80 2.8 SP-338 1 Vehicle Control 60 0.81 3.2 SP-338 2 Vanco. Positive Control 0 1.00 0 SP-338 3 10% fecal suspension 0 0.95 1 SP-338 5 N1957 2.0E+07 10 0.80 2 SP-338 6 N1957 2.0E+06 0 0.97 1 SP-338 7 N1957 2.0E+05 20 0.85 1.7 SP-338 11 N1957 2.0E+07 20 0.86 2 SP-338 12 N1957 2.0E+06 30 0.83 2.5 SP-338 13 N1961 2.0E+07 10 0.93 1.3 SP-338 14 N1955 2.0E+07 0 0.91 1.2 SP-338 15 N1955 2.0E+06 10 0.90 1.5 SP-338 16 N1955 2.0E+05 10 0.89 2.7 SP-338 17 N1967 2.0E+07 10 0.94 1.4 SP-338 18 N1983 2.0E+07 0 0.92 1 SP-338 19 N1989 2.0E+07 10 0.91 1.3 SP-338 20 N1996 2.0E+07 10 0.93 1.3 SP-338 21 Naïve 0 1.00 0 SP-339 1 Vehicle Control 20 0.88 2.2 SP-339 2 Vanco. Positive Control 0 0.99 0 SP-339 3 10% fecal suspension 0 0.97 0 SP-339 4 N1995 2.0E+07 20 0.83 2.1 SP-339 5 N1995 2.0E+06 10 0.91 1.5 SP-339 6 N1995 2.0E+05 0 0.96 1.2 SP-339 7 N1950 2.0E+07 0 0.94 1 SP-339 8 N1994 2.0E+07 20 0.87 1.8 SP-339 9 N1997 2.0E+07 0 0.95 1.2 SP-339 10 N1967 2.0E+07 0 0.93 1.2 SP-339 11 N1983 2.0E+07 10 0.83 2.2 SP-339 12 N1989 2.0E+07 0 0.88 1.5 SP-339 13 N1996 2.0E+07 0 0.97 1 SP-339 14 N2002 2.0E+07 20 0.92 2 SP-339 15 N2000 2.0E+07 0 0.98 1.2 SP-339 21 Naïve 0 0.98 0 SP-342 1 Vehicle Control 40 0.85 2.5 SP-342 2 Vanco. Positive Control 0 1.00 0 SP-342 5 N1957 2.0E+08 0 0.94 0.2 SP-342 6 N1957 2.0E+07 0 0.96 0 SP-342 7 N1957 2.0E+06 10 0.88 1.3 SP-342 8 N1980 2.0E+08 10 0.92 1.8 SP-342 9 N1998 2.0E+08 20 0.83 2.8 SP-342 10 N1976 2.0E+08 10 0.92 1.4 SP-342 11 N1987 2.0E+08 10 0.93 1.6 SP-342 12 N2005 2.0E+08 20 0.86 2.4 SP-342 13 N1958 2.0E+08 0 0.94 1.5 SP-342 14 N2004 2.0E+08 10 0.93 1.4 SP-342 15 N1949 2.0E+08 10 0.87 1.5 SP-342 18 N1970 2.0E+08 50 0.81 3 SP-342 21 Naïve 0 0.99 0 SP-361 1 Vehicle Control 30 0.88 2.6 SP-361 2 10% fecal suspension 0 0.99 0 SP-361 3 N435 1.0E+07 80 0.83 3.6 SP-361 4 N1979 1.0E+07 0 0.97 0 SP-361 5 N414 1.0E+07 0 0.97 0 SP-361 6 N512 1.0E+07 20 0.94 1.6 SP-361 7 N582 1.0E+07 10 0.93 0.9 SP-361 8 N571 1.0E+07 30 0.88 2.1 SP-361 9 N510 1.0E+07 0 0.93 0.3 SP-361 10 N1981 1.0E+07 40 0.83 2.8 SP-361 11 N1969 1.0E+07 80 0.82 3.6 SP-361 12 N461 1.0E+07 10 0.89 1.2 SP-361 13 N460 1.0E+07 0 0.93 1.1 SP-361 14 N1959 1.0E+07 30 0.89 1.9 SP-361 15 N2006 1.0E+07 30 0.89 1.9 SP-361 16 N1953 1.0E+07 10 0.83 2.3 SP-361 17 N1960 1.0E+07 0 0.92 1 SP-361 18 N2007 1.0E+07 10 0.91 0.9 SP-361 19 N1978 1.0E+07 10 0.91 1.3 SP-361 20 N1972 1.0E+07 30 0.83 2.6 SP-361 21 Naïve 0 1.00 0 SP-363 1 Vehicle Control 30 0.85 2.6 SP-363 2 10% fecal suspension 0 0.95 0 SP-363 8 N1974 1.0E+07 60 0.81 3.2 SP-363 9 N582 1.0E+07 60 0.81 3.2 SP-363 10 N435 1.0E+07 30 0.86 2.1 SP-363 11 N414 1.0E+07 40 0.83 2.5 SP-363 12 N457 1.0E+07 30 0.83 2.2 SP-363 13 N511 1.0E+07 20 0.87 2 SP-363 14 N513 1.0E+07 0 0.88 0.2 SP-363 15 N682 1.0E+07 30 0.82 2.6 SP-363 16 N736 1.0E+07 40 0.82 2.8 SP-363 17 N732 1.0E+07 10 0.86 1.3 SP-363 18 N1948 1.0E+07 60 0.85 3.2 SP-363 19 N853 1.0E+07 10 0.85 2.2 SP-363 20 N1979 1.0E+07 60 0.78 3.2 SP-363 21 N879 1.0E+07 40 0.83 2.8 SP-363 22 N999 1.0E+07 20 0.88 2.4 SP-363 23 N975 1.0E+07 30 0.80 2.6 SP-363 24 N861 1.0E+07 50 0.85 3 SP-363 25 N1095 1.0E+07 80 0.83 3.6 SP-363 26 Naïve 0 1.00 0 SP-364 1 Vehicle Control 40 0.83 2.8 SP-364 4 N582 1.0E+07 0 0.81 0.9 SP-364 5 N582 1.0E+06 0 0.84 0.9 SP-364 6 N582 1.0E+05 40 0.76 2.5 SP-364 13 N414 1.0E+07 0 0.84 0 SP-364 14 N414 1.0E+06 30 0.79 2.4 SP-364 15 N414 1.0E+05 10 0.76 2 SP-364 22 10% fecal suspension 0 0.97 0 SP-364 23 Naïve 0 0.99 0 SP-365 1 Vehicle Control 40 0.83 2.8 SP-365 4 10% fecal suspension 0 0.98 0 SP-365 13 N582 1.0E+07 60 0.80 3.2 SP-365 14 N582 1.0E+06 10 0.89 1.5 SP-365 15 N414 1.0E+07 20 0.86 1.7 SP-365 16 N414 1.0E+06 80 0.83 3.5 SP-365 21 Naïve 0 1.00 0 SP-366 1 Vehicle Control 20 0.82 2.4 SP-366 4 10% fecal suspension 0 0.93 1 SP-366 7 N582 1.0E+07 0 0.86 1 SP-366 10 N414 1.0E+07 20 0.83 2.4 SP-366 13 N402 1.0E+07 30 0.81 2.1 SP-366 16 N1982 1.0E+07 0 0.90 1.1 SP-366 19 N460 1.0E+07 10 0.83 2.2 SP-366 22 N513 6.7E+06 40 0.82 2.8 SP-366 23 N1966 1.0E+07 0 0.90 0.5 SP-366 24 N1977 1.0E+07 20 0.83 1.9 SP-366 25 N1979 1.0E+07 20 0.83 2.4 SP-366 26 N682 1.0E+07 20 0.83 2.3 SP-366 27 N1947 1.0E+07 10 0.82 1.3 SP-366 28 N582 1.0E+07 20 0.82 1.8 SP-366 29 N414 1.0E+07 0 0.85 1.5 SP-366 30 N603 1.0E+07 30 0.82 2.2 SP-366 31 Naïve 0 0.99 0 SP-368 1 Vehicle Control 50 0.85 2.8 SP-368 2 10% fecal suspension 0 0.97 0 SP-368 3 Ethanol-treated fecal spores A 20 0.90 1.8 SP-368 7 N1966 1.0E+07 0 0.89 1 SP-368 8 N1966 1.0E+06 10 0.91 1.5 SP-368 9 N1966 1.0E+05 50 0.82 3.1 SP-368 10 Ethanol-treated fecal spores B 0 0.99 0 SP-368 15 Ethanol-treated fecal spores C 0 0.95 1 SP-368 21 Naïve 0 1.00 0 SP-374 1 Vehicle Control 100 0.83 4 SP-374 4 10% fecal suspension 10 0.89 0.5 SP-374 11 N1966 1.0E+08 0 0.87 1 SP-374 12 N1966 1.0E+08 0 0.91 0.5 SP-374 13 N1966 1.0E+07 10 0.88 1.3 SP-374 14 N1966 1.0E+06 50 0.79 3 SP-374 15 N584 1.0E+08 0 0.89 1 SP-374 16 N584 1.0E+07 30 0.84 2.4 SP-374 17 N1962 1.0E+07 0 0.93 0 SP-374 18 N382 1.0E+07 10 0.85 1.5 SP-374 19 N1964 1.0E+07 20 0.89 1.8 SP-374 20 N1965 1.0E+07 30 0.85 2.1 SP-374 21 N306 1.0E+07 10 0.90 0.4 SP-374 22 N1988 1.0E+07 0 0.89 1 SP-374 23 N2003 1.0E+07 0 0.92 1.2 SP-374 24 N1993 1.0E+07 20 0.77 2.4 SP-374 25 Naïve 0 0.99 0 SP-376 1 Vehicle Control 60 0.83 3.2 SP-376 2 10% fecal suspension 0 0.98 0 SP-376 3 N1966 1.0E+08 30 0.79 2.4 SP-376 4 N1966 1.0E+07 0 0.95 0 SP-376 5 N1966 1.0E+08 30 0.79 2.6 SP-376 6 N1966 1.0E+07 10 0.88 2.2 SP-376 7 N1986 1.0E+07 40 0.80 2.8 SP-376 8 N1962 1.0E+08 0 0.98 0 SP-376 9 N1962 1.0E+07 0 0.95 0 SP-376 10 N1963 1.0E+07 40 0.81 2.6 SP-376 11 N1984 1.0E+08 0 0.97 0 SP-376 12 N1984 1.0E+07 0 0.90 1.1 SP-376 13 N1990 1.0E+08 0 0.92 1 SP-376 14 N1990 1.0E+07 0 0.92 1 SP-376 15 N1999 1.0E+08 10 0.87 1.4 SP-376 16 N1999 1.0E+07 0 0.93 0 SP-376 17 N1968 1.0E+07 50 0.78 3 SP-376 18 N1951 1.0E+07 0 0.93 1 SP-376 19 N1991 1.0E+07 0 0.93 1.1 SP-376 20 N1975 1.0E+07 50 0.78 3 SP-376 21 Naïve 0 0.99 0 SP-383 1 Vehicle Control 100 0.83 4 SP-383 2 10% fecal suspension 0 0.92 0.1 SP-383 9 N1962 1.0E+09 10 0.95 1.3 SP-383 10 N1962 1.0E+08 10 0.93 1.3 SP-383 11 N1962 1.0E+07 0 0.92 1 SP-383 12 N1984 1.0E+09 0 0.89 1 SP-383 13 N1984 1.0E+08 10 0.94 1.3 SP-383 14 N1984 1.0E+07 10 0.90 1.3 SP-383 21 Naïve 0 1.00 0 SP-390 1 Vehicle Control 80 0.82 3.6 SP-390 2 10% fecal suspension 0 0.98 0.1 SP-390 3 N1962 2.0E+07 0 0.97 0 SP-390 4 N1962 2.0E+06 0 0.98 0 SP-390 5 N1984 2.0E+07 0 0.95 1 SP-390 6 N1984 2.0E+06 0 0.95 0.1 SP-390 9 N1962 2.0E+07 0 0.93 1 SP-390 10 N1962 2.0E+06 10 0.93 1.3 SP-390 11 N1984 2.0E+07 20 0.86 2.2 SP-390 12 N1984 2.0E+06 30 0.88 2.1 SP-390 13 N1952 2.0E+07 0 0.89 1 SP-390 14 N2001 2.0E+07 0 0.95 0.2 SP-390 15 N1973 2.0E+07 10 0.90 0.7 SP-390 16 N1954 2.0E+07 0 0.94 1.1 SP-390 17 N1985 2.0E+07 10 0.86 1.8 SP-390 18 N1971 2.0E+07 0 0.89 0.9 SP-390 19 N1956 2.0E+07 0 0.95 0 SP-390 20 N1992 2.0E+07 0 0.95 0 SP-390 31 Naïve 0 0.98 0

Efficacy of Network Ecologies screened in Clostridium difficile Infection Prevention Mouse Model.

TABLE 17 Network Ecology ID Exemplary Network Clades Exemplary Network OTUs Exemplary Keystone OTUs N306 clade_252, (clade_260 or clade_260c or Blautia producta, Clostridium hylemonae, Coprococcus comes, Eubacterium clade_260g or clade_260h), (clade_262 Clostridium innocuum, Clostridium rectale, Faecalibacterium prausnitzii, or clade_262i), (clade_309 or clade_309c orbiscindens, Clostridium symbiosum, Ruminococcus obeum, Ruminococcus or clade_309e or clade_309g or Clostridium tertium, Collinsella torques clade_309h or clade_309i), (clade_351 or aerofaciens, Coprobacillus sp. D7, clade_351e), (clade_38 or clade_38e or Coprococcus comes, Eubacterium rectale, clade_38i), (clade_408 or clade_408b or Eubacterium sp. WAL 14571, clade_408d or clade_408f or clade_408g Faecalibacterium prausnitzii, or clade_408h), (clade_444 or Lachnospiraceae bacterium 5_1_57FAA, clade_444i), (clade_478 or clade_478i), Roseburia faecalis, Ruminococcus (clade_481 or clade_481a or clade_481b obeum, Ruminococcus torques or clade_481e or clade_481g or clade_481h or clade_481i), clade_494, (clade_553 or clade_553i) N382 clade_252, (clade_260 or clade_260c or Blautia producta, Clostridium hylemonae, Coprococcus comes, Ruminococcus clade_260g or clade_260h), (clade_262 Clostridium innocuum, Clostridium bromii or clade_262i), (clade_309 or clade_309c orbiscindens, Clostridium symbiosum, or clade_309e or clade_309g or Clostridium tertium, Collinsella clade_309h or clade_309i), (clade_351 or aerofaciens, Coprococcus comes, clade_351e), (clade_360 or clade_360c or Lachnospiraceae bacterium 5_1_57FAA, clade_360g or clade_360h or clade_360i), Ruminococcus bromii, Ruminococcus (clade_408 or clade_408b or clade_408d gnavus or clade_408f or clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N402 (clade_262 or clade_262i), clade_286, Alistipes shahii, Coprococcus comes, Alistipes shahii, Coprococcus comes, (clade_309 or clade_309c or clade_309e Dorea formicigenerans, Dorea Dorea formicigenerans, Dorea or clade_309g or clade_309h or longicatena, Eubacterium rectale, longicatena, Eubacterium rectale, clade_309i), (clade_360 or clade_360c or Faecalibacterium prausnitzii, Odoribacter Faecalibacterium prausnitzii, clade_360g or clade_360h or clade_360i), splanchnicus, Parabacteroides merdae, Odoribacter splanchnicus, (clade_444 or clade_444i), clade_466, Ruminococcus obeum, Ruminococcus Parabacteroides merdae, Ruminococcus (clade_478 or clade_478i), clade_500 torques obeum, Ruminococcus torques N414 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Dorea longicatena, formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 Eubacterium eligens, Eubacterium Eubacterium eligens, Eubacterium or clade_360c or clade_360g or rectale, Faecalibacterium prausnitzii, rectale, Faecalibacterium prausnitzii, clade_360h or clade_360i), (clade_444 or Odoribacter splanchnicus, Ruminococcus Odoribacter splanchnicus, clade_444i), clade_466, (clade_478 or obeum, Ruminococcus torques Ruminococcus obeum, Ruminococcus clade_478i), (clade_522 or clade_522i) torques N435 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Dorea longicatena, formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 Eubacterium rectale, Faecalibacterium Eubacterium rectale, Faecalibacterium or clade_360c or clade_360g or prausnitzii, Odoribacter splanchnicus, prausnitzii, Odoribacter splanchnicus, clade_360h or clade_360i), (clade_444 or Ruminococcus obeum, Ruminococcus Ruminococcus obeum, Ruminococcus clade_444i), clade_466, (clade_478 or torques torques clade_478i) N457 (clade_262 or clade_262i), (clade_309 or Dorea longicatena, Eubacterium eligens, Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g Eubacterium rectale, Faecalibacterium eligens, Eubacterium rectale, or clade_309h or clade_309i), (clade_360 prausnitzii, Roseburia intestinalis, Faecalibacterium prausnitzii, Roseburia or clade_360c or clade_360g or Ruminococcus obeum, Ruminococcus intestinalis, Ruminococcus obeum, clade_360h or clade_360i), (clade_444 or torques Ruminococcus torques clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N460 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Eubacterium rectale, formicigenerans, Eubacterium rectale, or clade_309h or clade_309i), (clade_360 Faecalibacterium prausnitzii, Odoribacter Faecalibacterium prausnitzii, or clade_360c or clade_360g or splanchnicus, Ruminococcus obeum, Odoribacter splanchnicus, clade_360h or clade_360i), (clade_444 or Ruminococcus torques Ruminococcus obeum, Ruminococcus clade_444i), clade_466, (clade_478 or torques clade_478i) N461 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Dorea longicatena, formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 Eubacterium rectale, Faecalibacterium Eubacterium rectale, Faecalibacterium or clade_360c or clade_360g or prausnitzii, Ruminococcus obeum, prausnitzii, Ruminococcus obeum, clade_360h or clade_360i), (clade_444 or Ruminococcus torques Ruminococcus torques clade_444i), (clade_478 or clade_478i) N510 (clade_262 or clade_262i), (clade_309 or Dorea longicatena, Eubacterium eligens, Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g Eubacterium rectale, Faecalibacterium eligens, Eubacterium rectale, or clade_309h or clade_309i), (clade_360 prausnitzii, Ruminococcus obeum, Faecalibacterium prausnitzii, or clade_360c or clade_360g or Ruminococcus torques Ruminococcus obeum, Ruminococcus clade_360h or clade_360i), (clade_444 or torques clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N511 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Eubacterium rectale, Coprococcus comes, Eubacterium clade_309c or clade_309e or clade_309g Faecalibacterium prausnitzii, Roseburia rectale, Faecalibacterium prausnitzii, or clade_309h or clade_309i), (clade_444 intestinalis, Ruminococcus obeum, Roseburia intestinalis, Ruminococcus or clade_444i), (clade_478 or clade_478i) Ruminococcus torques obeum, Ruminococcus torques N512 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Dorea longicatena, formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 Eubacterium rectale, Ruminococcus Eubacterium rectale, Ruminococcus or clade_360c or clade_360g or obeum, Ruminococcus torques obeum, Ruminococcus torques clade_360h or clade_360i), (clade_444 or clade_444i) N513 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Eubacterium rectale, formicigenerans, Eubacterium rectale, or clade_309h or clade_309i), (clade_360 Faecalibacterium prausnitzii, Faecalibacterium prausnitzii, or clade_360c or clade_360g or Ruminococcus obeum, Ruminococcus Ruminococcus obeum, Ruminococcus clade_360h or clade_360i), (clade_444 or torques torques clade_444i), (clade_478 or clade_478i) N571 (clade_262 or clade_262i), (clade_309 or Dorea longicatena, Eubacterium rectale, Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g Faecalibacterium prausnitzii, rectale, Faecalibacterium prausnitzii, or clade_309h or clade_309i), (clade_360 Ruminococcus obeum, Ruminococcus Ruminococcus obeum, Ruminococcus or clade_360c or clade_360g or torques torques clade_360h or clade_360i), (clade_444 or clade_444i), (clade_478 or clade_478i) N582 (clade_262 or clade_262i), (clade_309 or Clostridium symbiosum, Eubacterium Eubacterium rectale, Faecalibacterium clade_309c or clade_309e or clade_309g rectale, Faecalibacterium prausnitzii, prausnitzii, Ruminococcus obeum, or clade_309h or clade_309i), (clade_408 Ruminococcus obeum, Ruminococcus Ruminococcus torques or clade_408b or clade_408d or torques clade_408f or clade_408g or clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i) N584 (clade_260 or clade_260c or clade_260g Blautia producta, Clostridium Coprococcus comes or clade_260h), (clade_262 or symbiosum, Collinsella aerofaciens, clade_262i), (clade_309 or clade_309c or Coprococcus comes, Lachnospiraceae clade_309e or clade_309g or clade_309h bacterium 5_1_57FAA or clade_309i), (clade_408 or clade_408b or clade_408d or clade_408f or clade_408g or clade_408h), (clade_553 or clade_553i) N603 (clade_172 or clade_172i), (clade_309 or Bifidobacterium adolescentis, Dorea Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g longicatena, Eubacterium rectale, rectale, Faecalibacterium prausnitzii, or clade_309h or clade_309i), (clade_360 Faecalibacterium prausnitzii, Ruminococcus obeum or clade_360c or clade_360g or Ruminococcus obeum clade_360h or clade_360i), (clade_444 or clade_444i), (clade_478 or clade_478i) N682 clade_170, (clade_309 or clade_309c or Bacteroides caccae, Eubacterium rectale, Bacteroides caccae, Eubacterium clade_309e or clade_309g or clade_309h Faecalibacterium prausnitzii, rectale, Faecalibacterium prausnitzii, or clade_309i), (clade_444 or Ruminococcus obeum Ruminococcus obeum clade_444i), (clade_478 or clade_478i) N732 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Faecalibacterium Coprococcus comes, Faecalibacterium clade_309c or clade_309e or clade_309g prausnitzii, Ruminococcus obeum, prausnitzii, Ruminococcus obeum, or clade_309h or clade_309i), (clade_478 Ruminococcus torques Ruminococcus torques or clade_478i) N736 (clade_262 or clade_262i), (clade_309 or Dorea longicatena, Faecalibacterium Dorea longicatena, Faecalibacterium clade_309c or clade_309e or clade_309g prausnitzii, Ruminococcus obeum, prausnitzii, Ruminococcus obeum, or clade_309h or clade_309i), (clade_360 Ruminococcus torques Ruminococcus torques or clade_360c or clade_360g or clade_360h or clade_360i), (clade_478 or clade_478i) N853 (clade_262 or clade_262i), (clade_444 or Eubacterium rectale, Faecalibacterium Eubacterium rectale, Faecalibacterium clade_444i), (clade_478 or clade_478i) prausnitzii, Ruminococcus torques prausnitzii, Ruminococcus torques N861 (clade_262 or clade_262i), (clade_309 or Clostridium hathewayi, Ruminococcus Ruminococcus obeum, Ruminococcus clade_309c or clade_309e or clade_309g obeum, Ruminococcus torques torques or clade_309h or clade_309i), (clade_408 or clade_408b or clade_408d or clade_408f or clade_408g or clade_408h) N879 (clade_309 or clade_309c or clade_309e Faecalibacterium prausnitzii, Roseburia Faecalibacterium prausnitzii, Roseburia or clade_309g or clade_309h or intestinalis, Ruminococcus obeum intestinalis, Ruminococcus obeum clade_309i), (clade_444 or clade_444i), (clade_478 or clade_478i) N975 clade_170, (clade_262 or clade_262i), Bacteroides caccae, Coprococcus comes, Bacteroides caccae, Coprococcus (clade_360 or clade_360c or clade_360g Dorea longicatena comes, Dorea longicatena or clade_360h clade_360i) N999 (clade_309 or clade_309c or clade_309e Dorea formicigenerans, Faecalibacterium Dorea formicigenerans, or clade_309g or clade_309h or prausnitzii, Ruminococcus obeum Faecalibacterium prausnitzii, clade_309i), (clade_360 or clade_360c or Ruminococcus obeum clade_360g or clade_360h or clade_360i), (clade_478 or clade_478i) N1095 (clade_444 or clade_444i), (clade_522 or Eubacterium eligens, Eubacterium rectale Eubacterium eligens, Eubacterium clade_522i) rectale N1947 (clade_262 or clade_262i), (clade_309 or Bacteroides sp. 3_1_23, Collinsella Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g aerofaciens, Dorea longicatena, rectale, Faecalibacterium prausnitzii, or clade_309h or clade_309i), (clade_360 Escherichia coli, Eubacterium rectale, Roseburia intestinalis, Ruminococcus or clade_360c or clade_360g or Faecalibacterium prausnitzii, Roseburia obeum, Ruminococcus torques clade_360h or clade_360i), (clade_38 or intestinalis, Ruminococcus obeum, clade_38e or clade_38i), (clade_444 or Ruminococcus torques clade_444i), (clade_478 or clade_478i), (clade_553 or clade_553i), (clade_92 or clade_92e or clade_92i) N1948 (clade_262 or clade_262i), (clade_38 or Bacteroides sp. 1_1_6, Bacteroides sp. Faecalibacterium prausnitzii, clade_38e or clade_38i), (clade_478 or 3_1_23, Faecalibacterium prausnitzii, Ruminococcus torques clade_478i), (clade_65 or clade_65e) Ruminococcus torques N1949 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 3_1_23, Bacteroides vulgatus, Blautia clade_309i), (clade_378 or clade_378e), producta, Enterococcus faecalis, (clade_38 or clade_38e or clade_38i), Erysipelotrichaceae bacterium 3_1_53, (clade_479 or clade_479c or clade_479g Escherichia coli or clade_479h), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1950 clade_253, (clade_309 or clade_309c or Bacteroides sp. 1_1_6, Bacteroides sp. clade_309e or clade_309g or clade_309h 3_1_23, Bacteroides vulgatus, Blautia or clade_309i), (clade_378 or producta, Clostridium disporicum, clade_378e), (clade_38 or clade_38e or Erysipelotrichaceae bacterium 3_1_53 clade_38i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_65 or clade_65e) N1951 (clade_260 or clade_260c or clade_260g Blautia producta, Clostridium bolteae, Coprococcus comes, Eubacterium or clade_260h), (clade_262 or Clostridium hylemonae, Clostridium rectale clade_262i), (clade_309 or clade_309c or symbiosum, Coprococcus comes, clade_309e or clade_309g or clade_309h Eubacterium rectale, Lachnospiraceae or clade_309i), (clade_360 or clade_360c bacterium 5_1_57FAA, Ruminococcus or clade_360g or clade_360h or gnavus clade_360i), (clade_408 or clade_408b or clade_408d or clade_408f or clade_408g or clade_408h), (clade_444 or clade_444i) N1952 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Collinsella aerofaciens, clade_360c or clade_360g or clade_360h Coprococcus comes, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or bromii, Ruminococcus gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1953 clade_253, (clade_262 or clade_262i), Bacteroides sp. 1_1_6, Bacteroides Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e vulgatus, Clostridium disporicum, formicigenerans, Eubacterium rectale, or clade_309g or clade_309h or Clostridium mayombei, Clostridium Faecalibacterium prausnitzii, clade_309i), (clade_354 or clade_354e), symbiosum, Coprobacillus sp. D7, Odoribacter splanchnicus, (clade_360 or clade_360c or clade_360g Coprococcus comes, Dorea Ruminococcus obeum or clade_360h or clade_360i), (clade_378 formicigenerans, Enterococcus faecalis, or clade_378e), (clade_408 or clade_408b Erysipelotrichaceae bacterium 3_1_53, or clade_408d or clade_408f or Escherichia coli, Eubacterium rectale, clade_408g or clade_408h), (clade_444 Faecalibacterium prausnitzii, Odoribacter or clade_444i), clade_466, (clade_478 or splanchnicus, Ruminococcus obeum clade_478i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1954 clade_252, clade_253, (clade_260 or Blautia sp. M25, Clostridium bolteae, Blautia sp. M25, Coprococcus comes, clade_260c or clade_260g or Clostridium butyricum, Clostridium Ruminococcus bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Collinsella aerofaciens, clade_360c or clade_360g or clade_360h Coprococcus comes, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or bromii, Ruminococcus gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1955 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 2_1_22, Bacteroides sp. 3_1_23, clade_309i), (clade_354 or clade_354e), Bacteroides vulgatus, Blautia producta, (clade_378 or clade_378e), (clade_38 or Citrobacter sp. 30_2, Clostridium clade_38e or clade_38i), (clade_479 or sordellii, Coprobacillus sp. D7, clade_479c or clade_479g or Enterococcus faecalis, Enterococcus clade_479h), (clade_481 or clade_481a or faecium, Erysipelotrichaceae bacterium clade_481b or clade_481e or clade_481g 3_1_53, Escherichia coli or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1956 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Clostridium nexile, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium nexile, clade_309i), (clade_351 or clade_351e), Clostridium orbiscindens, Clostridium (clade_354 or clade_354e), (clade_360 or symbiosum, Clostridium tertium, clade_360c or clade_360g or clade_360h Collinsella aerofaciens, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or bromii, Ruminococcus gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1957 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 3_1_23, Bacteroides vulgatus, Blautia clade_309i), (clade_351 or clade_351e), producta, Clostridium innocuum, (clade_354 or clade_354e), (clade_378 or Clostridium sordellii, Coprobacillus sp. clade_378e), (clade_38 or clade_38e or D7, Enterococcus faecalis, Escherichia clade_38i), (clade_481 or clade_481a or coli clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1958 (clade_351 or clade_351e), (clade_354 or Clostridium innocuum, Clostridium clade_354e), (clade_481 or clade_481a or sordellii, Coprobacillus sp. D7 clade_481b or clade_481e or clade_481g or clade_481h or clade_481i) N1959 clade_253, (clade_262 or clade_262i), Bacteroides sp. 1_1_6, Bacteroides sp. Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e 3_1_23, Bacteroides vulgatus, Blautia formicigenerans, Dorea longicatena, or clade_309g or clade_309h or producta, Clostridium disporicum, Eubacterium eligens, Eubacterium clade_309i), (clade_360 or clade_360c or Coprococcus comes, Dorea rectale, Faecalibacterium prausnitzii, clade_360g or clade_360h or clade_360i), formicigenerans, Dorea longicatena, Ruminococcus obeum, Ruminococcus (clade_378 or clade_378e), (clade_38 or Enterococcus faecalis, torques clade_38e or clade_38i), (clade_444 or Erysipelotrichaceae bacterium 3_1_53, clade_444i), (clade_478 or clade_478i), Escherichia coli, Eubacterium eligens, (clade_479 or clade_479c or clade_479g Eubacterium rectale, Faecalibacterium or clade_479h), (clade_497 or clade_497e prausnitzii, Ruminococcus obeum, or clade_497f), (clade_522 or Ruminococcus torques clade_522i), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1960 clade_253, (clade_262 or clade_262i), Clostridium disporicum, Clostridium Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e mayombei, Clostridium symbiosum, formicigenerans, Eubacterium rectale, or clade_309g or clade_309h or Coprobacillus sp. D7, Coprococcus Faecalibacterium prausnitzii, clade_309i), (clade_354 or clade_354e), comes, Dorea formicigenerans, Ruminococcus obeum (clade_360 or clade_360c or clade_360g Enterococcus faecalis, or clade_360h or clade_360i), (clade_408 Erysipelotrichaceae bacterium 3_1_53, or clade_408b or clade_408d or Escherichia coli, Eubacterium rectale, clade_408f or clade_408g or Faecalibacterium prausnitzii, clade_408h), (clade_444 or clade_444i), Ruminococcus obeum (clade_478 or clade_478i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_92 or clade_92e or clade_92i) N1961 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 3_1_23, Bacteroides vulgatus, Blautia clade_309i), (clade_351 or clade_351e), producta, Clostridium innocuum, (clade_378 or clade_378e), (clade_38 or Enterococcus faecalis, Escherichia coli clade_38e or clade_38i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1962 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Collinsella aerofaciens, clade_360c or clade_360g or clade_360h Coprococcus comes, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or bromii, Ruminococcus gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1963 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium Coprococcus comes, Ruminococcus clade_260c or clade_260g or disporicum, Clostridium hylemonae, bromii clade_260h), (clade_262 or clade_262i), Clostridium innocuum, Clostridium (clade_309 or clade_309c or clade_309e orbiscindens, Clostridium symbiosum, or clade_309g or clade_309h or Clostridium tertium, Collinsella clade_309i), (clade_351 or clade_351e), aerofaciens, Coprococcus comes, (clade_360 or clade_360c or clade_360g Lachnospiraceae bacterium 5_1_57FAA, or clade_360h or clade_360i), (clade_408 Ruminococcus bromii, Ruminococcus or clade_408b or clade_408d or gnavus clade_408f or clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1964 clade_170, (clade_260 or clade_260c or Alistipes shahii, Bacteroides caccae, Alistipes shahii, Bacteroides caccae, clade_260g or clade_260h), (clade_262 Bacteroides stercoris, Blautia producta, Bacteroides stercoris, Coprococcus or clade_262i), clade_286, (clade_309 or Clostridium hathewayi, Clostridium comes, Eubacterium rectale, clade_309c or clade_309e or clade_309g symbiosum, Collinsella aerofaciens, Holdemania filiformis, Parabacteroides or clade_309h or clade_309i), (clade_408 Coprococcus comes, Eubacterium rectale, merdae, Ruminococcus bromii, or clade_408b or clade_408d or Holdemania filiformis, Lachnospiraceae Ruminococcus obeum, Ruminococcus clade_408f or clade_408g or bacterium 5_1_57FAA, Parabacteroides torques clade_408h), (clade_444 or clade_444i), merdae, Ruminococcus bromii, clade_485, clade_500, clade_537, Ruminococcus obeum, Ruminococcus (clade_553 or clade_553i), clade_85 torques N1965 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Eubacterium clade_260c or clade_260g or Clostridium butyricum, Clostridium rectale, Faecalibacterium prausnitzii, clade_260h), (clade_262 or clade_262i), disporicum, Clostridium mayombei, Roseburia intestinalis, Ruminococcus (clade_309 or clade_309c or clade_309e Clostridium symbiosum, Collinsella bromii, Ruminococcus obeum or clade_309g or clade_309h or aerofaciens, Coprococcus comes, clade_309i), (clade_354 or clade_354e), Eubacterium rectale, Faecalibacterium (clade_408 or clade_408b or clade_408d prausnitzii, Lachnospiraceae bacterium or clade_408f or clade_408g or 5_1_57FAA, Roseburia intestinalis, clade_408h), (clade_444 or clade_444i), Ruminococcus bromii, Ruminococcus (clade_478 or clade_478i), clade_537, obeum (clade_553 or clade_553i) N1966 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes clade_260c or clade_260g or Clostridium butyricum, Clostridium clade_260h), (clade_262 or clade_262i), disporicum, Clostridium mayombei, (clade_309 or clade_309c or clade_309e Clostridium symbiosum, Collinsella or clade_309g or clade_309h or aerofaciens, Coprococcus comes, clade_309i), (clade_354 or clade_354e), Lachnospiraceae bacterium 5_1_57FAA (clade_408 or clade_408b or clade_408d or clade_408f or clade_408g or clade_408h), (clade_553 or clade_553i) N1967 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 3_1_23, Bacteroides vulgatus, Blautia clade_309i), (clade_378 or clade_378e), producta, Enterococcus faecium, (clade_38 or clade_38e or clade_38i), Escherichia coli (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1968 clade_252, clade_253, (clade_351 or Clostridium butyricum, Clostridium Faecalibacterium prausnitzii, clade_351e), (clade_354 or clade_354e), disporicum, Clostridium innocuum, Ruminococcus bromii (clade_478 or clade_478i), clade_494, Clostridium mayombei, Clostridium clade_537, (clade_553 or clade_553i) orbiscindens, Clostridium tertium, Collinsella aerofaciens, Faecalibacterium prausnitzii, Ruminococcus bromii N1969 clade_252, clade_253, (clade_262 or Blautia producta, Clostridium butyricum, Dorea formicigenerans, Ruminococcus clade_262i), (clade_309 or clade_309c or Clostridium disporicum, Clostridium torques clade_309e or clade_309g or clade_309h mayombei, Dorea formicigenerans, or clade_309i), (clade_354 or Erysipelotrichaceae bacterium 3_1_53, clade_354e), (clade_360 or clade_360c or Ruminococcus torques clade_360g or clade_360h or clade_360i), (clade_479 or clade_479c or clade_479g or clade_479h) N1970 (clade_351 or clade_351e), (clade_354 or Bacteroides sp. 1_1_6, Bacteroides sp. clade_354e), (clade_378 or clade_378e), 3_1_23, Bacteroides vulgatus, (clade_38 or clade_38e or clade_38i), Clostridium innocuum, Clostridium (clade_481 or clade_481a or clade_481b sordellii, Coprobacillus sp. D7, or clade_481e or clade_481g or Enterococcus faecalis, Escherichia coli clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1971 clade_252, clade_253, (clade_260 or Blautia producta, Blautia schinkii, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium bolteae, Clostridium bromii clade_260h), (clade_262 or clade_262i), butyricum, Clostridium disporicum, (clade_309 or clade_309c or clade_309e Clostridium hylemonae, Clostridium or clade_309g or clade_309h or innocuum, Clostridium mayombei, clade_309i), (clade_351 or clade_351e), Clostridium orbiscindens, Clostridium (clade_354 or clade_354e), (clade_360 or symbiosum, Clostridium tertium, clade_360c or clade_360g or clade_360h Collinsella aerofaciens, Coprococcus or clade_360i), (clade_408 or clade_408b comes, Lachnospiraceae bacterium or clade_408d or clade_408f or 5_1_57FAA, Ruminococcus bromii, clade_408g or clade_408h), clade_494, Ruminococcus gnavus clade_537, (clade_553 or clade_553i) N1972 clade_253, (clade_262 or clade_262i), Clostridium disporicum, Clostridium Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e mayombei, Clostridium symbiosum, formicigenerans, Eubacterium rectale, or clade_309g or clade_309h or Coprobacillus sp. D7, Coprococcus Faecalibacterium prausnitzii, clade_309i), (clade_354 or clade_354e), comes, Dorea formicigenerans, Ruminococcus obeum (clade_360 or clade_360c or clade_360g Erysipelotrichaceae bacterium 3_1_53, or clade_360h or clade_360i), (clade_408 Eubacterium rectale, Faecalibacterium or clade_408b or clade_408d or prausnitzii, Ruminococcus obeum clade_408f or clade_408g or clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i) N1973 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Coprococcus comes, clade_360c or clade_360g or clade_360h Lachnospiraceae bacterium 5_1_57FAA, or clade_360i), (clade_408 or clade_408b Ruminococcus bromii, Ruminococcus or clade_408d or clade_408f or gnavus clade_408g or clade_408h), clade_494, clade_537 N1974 (clade_262 or clade_262i), (clade_309 or Coprococcus comes, Dorea Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g formicigenerans, Dorea longicatena, formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 Eubacterium rectale, Faecalibacterium Eubacterium rectale, Faecalibacterium or clade_360c or clade_360g or prausnitzii, Odoribacter splanchnicus, prausnitzii, Odoribacter splanchnicus, clade_360h or clade_360i), (clade_444 or Roseburia intestinalis, Ruminococcus Roseburia intestinalis, Ruminococcus clade_444i), clade_466, (clade_478 or obeum, Ruminococcus torques obeum, Ruminococcus torques clade_478i) N1975 (clade_260 or clade_260c or clade_260g Blautia producta, Clostridium bolteae, Coprococcus comes, Eubacterium or clade_260h), (clade_262 or Clostridium hylemonae, Clostridium rectale, Faecalibacterium prausnitzii, clade_262i), (clade_309 or clade_309c or innocuum, Clostridium mayombei, Ruminococcus bromii clade_309e or clade_309g or clade_309h Clostridium orbiscindens, Clostridium or clade_309i), (clade_351 or symbiosum, Collinsella aerofaciens, clade_351e), (clade_354 or clade_354e), Coprococcus comes, Eubacterium rectale, (clade_360 or clade_360c or clade_360g Faecalibacterium prausnitzii, or clade_360h or clade_360i), (clade_408 Lachnospiraceae bacterium 5_1_57FAA, or clade_408b or clade_408d or Ruminococcus bromii, Ruminococcus clade_408f or clade_408g or gnavus clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i), clade_494, clade_537, (clade_553 or clade_553i) N1976 (clade_351 or clade_351e), (clade_378 or Bacteroides sp. 1_1_6, Bacteroides sp. clade_378e), (clade_38 or clade_38e or 3_1_23, Bacteroides vulgatus, clade_38i), (clade_481 or clade_481a or Clostridium innocuum, Coprobacillus sp. clade_481b or clade_481e or clade_481g D7, Enterococcus faecalis or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e) N1977 clade_252, clade_253, (clade_262 or Blautia producta, Clostridium butyricum, Dorea formicigenerans, Ruminococcus clade_262i), (clade_309 or clade_309c or Clostridium disporicum, Clostridium torques clade_309e or clade_309g or clade_309h mayombei, Dorea formicigenerans, or clade_309i), (clade_354 or Erysipelotrichaceae bacterium 3_1_53, clade_354e), (clade_360 or clade_360c or Eubacterium tenue, Ruminococcus clade_360g or clade_360h or clade_360i), torques (clade_479 or clade_479c or clade_479g or clade_479h) N1978 clade_253, (clade_262 or clade_262i), Bacteroides sp. 1_1_6, Bacteroides Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e vulgatus, Clostridium disporicum, formicigenerans, Eubacterium rectale, or clade_309g or clade_309h or Clostridium mayombei, Clostridium Faecalibacterium prausnitzii, clade_309i), (clade_354 or clade_354e), symbiosum, Coprobacillus sp. D7, Odoribacter splanchnicus, (clade_360 or clade_360c or clade_360g Coprococcus comes, Dorea Ruminococcus obeum or clade_360h or clade_360i), (clade_378 formicigenerans, Erysipelotrichaceae or clade_378e), (clade_408 or clade_408b bacterium 3_1_53, Escherichia coli, or clade_408d or clade_408f or Eubacterium rectale, Faecalibacterium clade_408g or clade_408h), (clade_444 prausnitzii, Odoribacter splanchnicus, or clade_444i), clade_466, (clade_478 or Ruminococcus obeum clade_478i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1979 (clade_262 or clade_262i), (clade_309 or Bacteroides sp. 1_1_6, Coprococcus Coprococcus comes, Dorea clade_309c or clade_309e or clade_309g comes, Dorea formicigenerans, Dorea formicigenerans, Dorea longicatena, or clade_309h or clade_309i), (clade_360 longicatena, Eubacterium rectale, Eubacterium rectale, Faecalibacterium or clade_360c or clade_360g or Faecalibacterium prausnitzii, prausnitzii, Ruminococcus obeum, clade_360h or clade_360i), (clade_444 or Ruminococcus obeum, Ruminococcus Ruminococcus torques clade_444i), (clade_478 or clade_478i), torques (clade_65 or clade_65e) N1980 (clade_309 or clade_309c or clade_309e Blautia producta, Clostridium innocuum, or clade_309g or clade_309h or Clostridium sordellii, Coprobacillus sp. clade_309i), (clade_351 or clade_351e), D7, Enterococcus faecalis, Escherichia (clade_354 or clade_354e), (clade_481 or coli clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_92 or clade_92e or clade_92i) N1981 (clade_262 or clade_262i), (clade_309 or Bacteroides sp. 3_1_23, Dorea Dorea longicatena, Eubacterium clade_309c or clade_309e or clade_309g longicatena, Eubacterium eligens, eligens, Eubacterium rectale, or clade_309h or clade_309i), (clade_360 Eubacterium rectale, Faecalibacterium Faecalibacterium prausnitzii, or clade_360c or clade_360g or prausnitzii, Ruminococcus obeum, Ruminococcus obeum, Ruminococcus clade_360h or clade_360i), (clade_38 or Ruminococcus torques torques clade_38e or clade_38i), (clade_444 or clade_444i), (clade_478 or clade_478i), (clade_522 or clade_522i) N1982 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Dorea clade_260c or clade_260g or Clostridium butyricum, Clostridium formicigenerans, Eubacterium rectale, clade_260h), (clade_262 or clade_262i), disporicum, Clostridium mayombei, Ruminococcus obeum, Ruminococcus (clade_309 or clade_309c or clade_309e Clostridium symbiosum, Collinsella torques or clade_309g or clade_309h or aerofaciens, Coprococcus comes, Dorea clade_309i), (clade_354 or clade_354e), formicigenerans, Erysipelotrichaceae (clade_360 or clade_360c or clade_360g bacterium 3_1_53, Eubacterium rectale, or clade_360h or clade_360i), (clade_408 Lachnospiraceae bacterium 5_1_57FAA, or clade_408b or clade_408d or Ruminococcus obeum, Ruminococcus clade_408f or clade_408g or torques clade_408h), (clade_444 or clade_444i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_553 or clade_553i) N1983 clade_252, clade_253, (clade_309 or Bacteroides sp. 1_1_6, Bacteroides sp. clade_309c or clade_309e or clade_309g 3_1_23, Bacteroides vulgatus, Blautia or clade_309h or clade_309i), (clade_354 producta, Clostridium butyricum, or clade_354e), (clade_378 or Clostridium disporicum, Clostridium clade_378e), (clade_38 or clade_38e or mayombei, Enterococcus faecium, clade_38i), (clade_479 or clade_479c or Erysipelotrichaceae bacterium 3_1_53, clade_479g or clade_479h), (clade_497 Escherichia coli or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1984 clade_253, (clade_260 or clade_260c or Blautia producta, Clostridium Eubacterium rectale clade_260g or clade_260h), (clade_309 disporicum, Clostridium innocuum, or clade_309c or clade_309e or Clostridium mayombei, Clostridium clade_309g or clade_309h or clade_309i), orbiscindens, Clostridium symbiosum, (clade_351 or clade_351e), (clade_354 or Collinsella aerofaciens, Eubacterium clade_354e), (clade_408 or clade_408b or rectale, Lachnospiraceae bacterium clade_408d or clade_408f or clade_408g 5_1_57FAA or clade_408h), (clade_444 or clade_444i), clade_494, (clade_553 or clade_553i) N1985 clade_252, clade_253, (clade_260 or Blautia glucerasei, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Collinsella aerofaciens, clade_360c or clade_360g or clade_360h Coprococcus comes, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or bromii, Ruminococcus gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N1986 clade_253, (clade_260 or clade_260c or Blautia producta, Clostridium Coprococcus comes clade_260g or clade_260h), (clade_262 disporicum, Clostridium symbiosum, or clade_262i), (clade_309 or clade_309c Collinsella aerofaciens, Coprococcus or clade_309e or clade_309g or comes, Lachnospiraceae bacterium clade_309h or clade_309i), (clade_408 or 5_1_57FAA clade_408b or clade_408d or clade_408f or clade_408g or clade_408h), (clade_553 or clade_553i) N1987 (clade_309 or clade_309c or clade_309e Blautia producta, Clostridium sordellii, or clade_309g or clade_309h or Escherichia coli clade_309i), (clade_354 or clade_354e), (clade_92 or clade_92e or clade_92i) N1988 clade_252, clade_253, (clade_260 or Alistipes shahii, Blautia producta, Alistipes shahii, Coprococcus comes, clade_260c or clade_260g or Clostridium bolteae, Clostridium Eubacterium rectale, Faecalibacterium clade_260h), (clade_262 or clade_262i), butyricum, Clostridium disporicum, prausnitzii, Holdemania filiformis, (clade_309 or clade_309c or clade_309e Clostridium mayombei, Clostridium Roseburia intestinalis, Ruminococcus or clade_309g or clade_309h or symbiosum, Collinsella aerofaciens, obeum, Ruminococcus torques clade_309i), (clade_354 or clade_354e), Coprococcus comes, Eubacterium rectale, (clade_408 or clade_408b or clade_408d Faecalibacterium prausnitzii, Holdemania or clade_408f or clade_408g or filiformis, Lachnospiraceae bacterium clade_408h), (clade_444 or clade_444i), 5_1_57FAA, Roseburia intestinalis, (clade_478 or clade_478i), clade_485, Ruminococcus obeum, Ruminococcus clade_500, (clade_553 or clade_553i) torques N1989 clade_252, clade_253, (clade_262 or Bacteroides sp. 1_1_6, Bacteroides sp. Dorea formicigenerans, Ruminococcus clade_262i), (clade_309 or clade_309c or 3_1_23, Bacteroides vulgatus, Blautia torques clade_309e or clade_309g or clade_309h producta, Clostridium butyricum, or clade_309i), (clade_354 or Clostridium disporicum, Clostridium clade_354e), (clade_360 or clade_360c or mayombei, Dorea formicigenerans, clade_360g or clade_360h or clade_360i), Enterococcus faecium, (clade_378 or clade_378e), (clade_38 or Erysipelotrichaceae bacterium 3_1_53, clade_38e or clade_38i), (clade_479 or Escherichia coli, Eubacterium tenue, clade_479c or clade_479g or Ruminococcus torques clade_479h), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1990 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium Coprococcus comes, Eubacterium clade_260c or clade_260g or disporicum, Clostridium hylemonae, rectale, Faecalibacterium prausnitzii, clade_260h), (clade_262 or clade_262i), Clostridium innocuum, Clostridium Ruminococcus bromii (clade_309 or clade_309c or clade_309e orbiscindens, Clostridium symbiosum, or clade_309g or clade_309h or Clostridium tertium, Collinsella clade_309i), (clade_351 or clade_351e), aerofaciens, Coprococcus comes, (clade_360 or clade_360c or clade_360g Eubacterium rectale, Faecalibacterium or clade_360h or clade_360i), (clade_408 prausnitzii, Lachnospiraceae bacterium or clade_408b or clade_408d or 5_1_57FAA, Ruminococcus bromii, clade_408f or clade_408g or Ruminococcus gnavus clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i), clade_494, clade_537, (clade_553 or clade_553i) N1991 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Eubacterium clade_260c or clade_260g or Clostridium butyricum, Clostridium rectale clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium symbiosum, clade_309i), (clade_351 or clade_351e), Clostridium tertium, Collinsella (clade_354 or clade_354e), (clade_360 or aerofaciens, Coprococcus comes, clade_360c or clade_360g or clade_360h Eubacterium rectale, Lachnospiraceae or clade_360i), (clade_408 or clade_408b bacterium 5_1_57FAA, Ruminococcus or clade_408d or clade_408f or gnavus clade_408g or clade_408h), (clade_444 or clade_444i), (clade_553 or clade_553i) N1992 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Lachnospiraceae bacterium clade_260c or clade_260g or Clostridium butyricum, Clostridium 1_4_56FAA, Ruminococcus bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium innocuum, Clostridium or clade_309g or clade_309h or mayombei, Clostridium orbiscindens, clade_309i), (clade_351 or clade_351e), Clostridium symbiosum, Clostridium (clade_354 or clade_354e), (clade_360 or tertium, Collinsella aerofaciens, clade_360c or clade_360g or clade_360h Lachnospiraceae bacterium 1_4_56FAA, or clade_360i), (clade_408 or clade_408b Lachnospiraceae bacterium 5_1_57FAA, or clade_408d or clade_408f or Ruminococcus bromii, Ruminococcus clade_408g or clade_408h), clade_494, gnavus clade_537, (clade_553 or clade_553i) N1993 clade_110, clade_170, (clade_378 or Bacteroides caccae, Bacteroides Bacteroides caccae, Bacteroides clade_378e), (clade_38 or clade_38e or eggerthii, Bacteroides sp. 1_1_6, eggerthii, Bacteroides stercoris, clade_38i), (clade_65 or clade_65e), Bacteroides sp. 3_1_23, Bacteroides Bacteroides uniformis clade_85 stercoris, Bacteroides uniformis, Bacteroides vulgatus N1994 clade_253, (clade_378 or clade_378e), Bacteroides sp. 1_1_6, Bacteroides sp. (clade_38 or clade_38e or clade_38i), 3_1_23, Bacteroides vulgatus, (clade_479 or clade_479c or clade_479g Clostridium disporicum, Enterococcus or clade_479h), (clade_497 or clade_497e faecium, Erysipelotrichaceae bacterium or clade_497f), (clade_65 or clade_65e), 3_1_53, Escherichia coli (clade_92 or clade_92e or clade_92i) N1995 clade_253, (clade_309 or clade_309c or Bacteroides sp. 1_1_6, Bacteroides sp. clade_309e or clade_309g or clade_309h 3_1_23, Bacteroides vulgatus, Blautia or clade_309i), (clade_378 or producta, Clostridium disporicum, clade_378e), (clade_38 or clade_38e or Enterococcus faecium, clade_38i), (clade_479 or clade_479c or Erysipelotrichaceae bacterium 3_1_53, clade_479g or clade_479h), (clade_497 Escherichia coli or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N1996 clade_253, (clade_309 or clade_309c or Blautia producta, Clostridium clade_309e or clade_309g or clade_309h disporicum, Erysipelotrichaceae or clade_309i), (clade_479 or clade_479c bacterium 3_1_53 or clade_479g or clade_479h) N1997 clade_253, (clade_309 or clade_309c or Blautia producta, Clostridium clade_309e or clade_309g or clade_309h disporicum, Enterococcus faecium, or clade_309i), (clade_479 or clade_479c Erysipelotrichaceae bacterium 3_1_53, or clade_479g or clade_479h), Escherichia coli (clade_497 or clade_497e or clade_497f), (clade_92 or clade_92e or clade_92i) N1998 (clade_378 or clade_378e), (clade_38 or Bacteroides sp. 1_1_6, Bacteroides sp. clade_38e or clade_38i), (clade_65 or 3_1_23, Bacteroides vulgatus clade_65e) N1999 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Eubacterium clade_260c or clade_260g or Clostridium butyricum, Clostridium rectale, Faecalibacterium prausnitzii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium mayombei, (clade_309 or clade_309c or clade_309e Clostridium symbiosum, Collinsella or clade_309g or clade_309h or aerofaciens, Coprococcus comes, clade_309i), (clade_354 or clade_354e), Eubacterium rectale, Faecalibacterium (clade_408 or clade_408b or clade_408d prausnitzii, Lachnospiraceae bacterium or clade_408f or clade_408g or 5_1_57FAA clade_408h), (clade_444 or clade_444i), (clade_478 or clade_478i), (clade_553 or clade_553i) N2000 clade_252, clade_253, (clade_262 or Blautia producta, Clostridium butyricum, Dorea formicigenerans, Ruminococcus clade_262i), (clade_309 or clade_309c or Clostridium disporicum, Clostridium torques clade_309e or clade_309g or clade_309h mayombei, Dorea formicigenerans, or clade_309i), (clade_354 or Erysipelotrichaceae bacterium 3_1_53, clade_354e), (clade_360 or clade_360c or Eubacterium tenue, Ruminococcus clade_360g or clade_360h or clade_360i), torques (clade_479 or clade_479c or clade_479g or clade_479h) N2001 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium disporicum, Clostridium bromii clade_260h), (clade_262 or clade_262i), hylemonae, Clostridium innocuum, (clade_309 or clade_309c or clade_309e Clostridium mayombei, Clostridium or clade_309g or clade_309h or orbiscindens, Clostridium symbiosum, clade_309i), (clade_351 or clade_351e), Clostridium tertium, Collinsella (clade_354 or clade_354e), (clade_360 or aerofaciens, Coprococcus comes, clade_360c or clade_360g or clade_360h Lachnospiraceae bacterium 5_1_57FAA, or clade_360i), (clade_408 or clade_408b Ruminococcus bromii, Ruminococcus or clade_408d or clade_408f or gnavus clade_408g or clade_408h), clade_494, clade_537, (clade_553 or clade_553i) N2002 clade_252, clade_253, (clade_309 or Blautia producta, Clostridium butyricum, clade_309c or clade_309e or clade_309g Clostridium disporicum, Clostridium or clade_309h or clade_309i), (clade_354 mayombei, Erysipelotrichaceae bacterium or clade_354e), (clade_479 or clade_479c 3_1_53 or clade_479g or clade_479h) N2003 clade_252, clade_253, (clade_260 or Blautia producta, Clostridium bolteae, Coprococcus comes, Ruminococcus clade_260c or clade_260g or Clostridium butyricum, Clostridium bromii clade_260h), (clade_262 or clade_262i), disporicum, Clostridium hylemonae, (clade_309 or clade_309c or clade_309e Clostridium mayombei, Clostridium or clade_309g or clade_309h or sordellii, Clostridium symbiosum, clade_309i), (clade_354 or clade_354e), Clostridium tertium, Collinsella (clade_360 or clade_360c or clade_360g aerofaciens, Coprobacillus sp. D7, or clade_360h or clade_360i), (clade_38 Coprococcus comes, Eubacterium sp. or clade_38e or clade_38i), (clade_408 or WAL 14571, Lachnospiraceae bacterium clade_408b or clade_408d or clade_408f 5_1_57FAA, Ruminococcus bromii, or clade_408g or clade_408h), Ruminococcus gnavus (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), clade_537, (clade_553 or clade_553i) N2004 (clade_351 or clade_351e), (clade_378 or Bacteroides sp. 1_1_6, Bacteroides sp. clade_378e), (clade_38 or clade_38e or 3_1_23, Bacteroides vulgatus, clade_38i), (clade_497 or clade_497e or Clostridium innocuum, Enterococcus clade_497f), (clade_65 or clade_65e), faecalis, Escherichia coli (clade_92 or clade_92e or clade_92i) N2005 (clade_309 or clade_309c or clade_309e Bacteroides sp. 1_1_6, Bacteroides sp. or clade_309g or clade_309h or 3_1_23, Bacteroides vulgatus, Blautia clade_309i), (clade_378 or clade_378e), producta, Enterococcus faecalis, (clade_38 or clade_38e or clade_38i), Escherichia coli (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e), (clade_92 or clade_92e or clade_92i) N2006 clade_170, (clade_262 or clade_262i), Bacteroides caccae, Bacteroides sp. Bacteroides caccae, Coprococcus (clade_309 or clade_309c or clade_309e 1_1_6, Coprococcus comes, Dorea comes, Dorea formicigenerans, Dorea or clade_309g or clade_309h or formicigenerans, Dorea longicatena, longicatena, Eubacterium rectale, clade_309i), (clade_360 or clade_360c or Eubacterium rectale, Faecalibacterium Faecalibacterium prausnitzii, clade_360g or clade_360h or clade_360i), prausnitzii, Ruminococcus obeum, Ruminococcus obeum, Ruminococcus (clade_444 or clade_444i), (clade_478 or Ruminococcus torques torques clade_478i), (clade_65 or clade_65e) N2007 clade_253, (clade_262 or clade_262i), Bacteroides sp. 1_1_6, Bacteroides Coprococcus comes, Dorea (clade_309 or clade_309c or clade_309e vulgatus, Clostridium disporicum, formicigenerans, Eubacterium rectale, or clade_309g or clade_309h or Clostridium mayombei, Clostridium Faecalibacterium prausnitzii, clade_309i), (clade_354 or clade_354e), symbiosum, Coprobacillus sp. D7, Odoribacter splanchnicus, (clade_360 or clade_360c or clade_360g Coprococcus comes, Dorea Ruminococcus obeum or clade_360h or clade_360i), (clade_378 formicigenerans, Enterococcus faecalis, or clade_378e), (clade_408 or clade_408b Erysipelotrichaceae bacterium 3_1_53, or clade_408d or clade_408f or Eubacterium rectale, Faecalibacterium clade_408g or clade_408h), (clade_444 prausnitzii, Odoribacter splanchnicus, or clade_444i), clade_466, (clade_478 or Ruminococcus obeum clade_478i), (clade_479 or clade_479c or clade_479g or clade_479h), (clade_481 or clade_481a or clade_481b or clade_481e or clade_481g or clade_481h or clade_481i), (clade_497 or clade_497e or clade_497f), (clade_65 or clade_65e)

Network Ecologies Screened In Vivo in Clostridium difficile Infection Prevention Mouse Model

TABLE 18 Net ID F-Score KEGG Orthology Pathways N253 29 KO: K00004, KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K01908, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N250 29 KO: K00004, KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K01908, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N249 29 KO: K00004, KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K01908, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N252 29 KO: K00004, KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K01908, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N251 28 KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K01908, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N257 27 KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N254 27 KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N255 27 KO: K00023, KO: K00101, KO: K00102, KO: K00116, KO: K00156, KO: K00158, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01720, KO: K01734, KO: K01905, KO: K01907, KO: K03366, KO: K03416, KO: K03417, KO: K03777, KO: K03778, KO: K03821, KO: K04020, KO: K05973 N1036 17 KO: K00101, KO: K00116, KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K00932, KO: K01069, KO: K01442, KO: K01659, KO: K01720, KO: K01734, KO: K01908, KO: K03417, KO: K03777, KO: K03778, KO: K04020 N968 17 KO: K00101, KO: K00116, KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K00932, KO: K01069, KO: K01442, KO: K01659, KO: K01720, KO: K01734, KO: K01908, KO: K03417, KO: K03777, KO: K03778, KO: K04020 N335 15 KO: K00102, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778, KO: K13923 N329 15 KO: K00102, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778, KO: K13923 N365 13 KO: K00004, KO: K00116, KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N363 13 KO: K00004, KO: K00116, KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N282 13 KO: K00004, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N280 13 KO: K00004, KO: K00116, KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N306 13 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03417, KO: K03778, KO: K07246 N623 12 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K13923 N350 12 KO: K00102, KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N324 12 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N914 12 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K13923 N351 12 KO: K00102, KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N296 12 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N917 12 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K13923 N299 12 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N790 12 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K13923 N386 12 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N275 12 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N777 12 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K13923 N318 12 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N271 12 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N816 12 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N256 12 KO: K00102, KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N259 12 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K07246 N262 12 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N382 12 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K01905, KO: K03417, KO: K03778, KO: K07246 N424 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N640 11 KO: K00102, KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N505 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N590 11 KO: K00004, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N641 11 KO: K00004, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N625 11 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N410 11 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K07246 N586 11 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N326 11 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01734, KO: K03778 N522 11 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K01896, KO: K03417, KO: K03778, KO: K07246 N265 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N588 11 KO: K00102, KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N1074 11 KO: K00004, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N610 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N408 11 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K07246 N548 11 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N383 11 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N269 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N901 11 KO: K00004, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N419 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N443 11 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01734, KO: K03778 N470 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N908 11 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N631 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N619 11 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N926 11 KO: K00004, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N429 11 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01659, KO: K01734, KO: K03778 N390 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N368 11 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N345 11 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N354 11 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N825 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N822 11 KO: K00004, KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N573 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N666 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N288 11 KO: K00156, KO: K00158, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N650 11 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N338 11 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N381 11 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N292 11 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N818 11 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N516 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N515 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N276 11 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N258 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N851 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01734, KO: K03778, KO: K04020, KO: K07246 N307 11 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N400 11 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N361 10 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N558 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N891 10 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K01905, KO: K03778, KO: K07246 N904 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N274 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N612 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N501 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N643 10 KO: K00156, KO: K00158, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N633 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N866 10 KO: K00102, KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K01905, KO: K03778 N444 10 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01734, KO: K03778 N535 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N552 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1072 10 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K01905, KO: K03778, KO: K07246 N597 10 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N539 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N717 10 KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N471 10 KO: K00156, KO: K00158, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N268 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N298 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N409 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N489 10 KO: K00156, KO: K00158, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N266 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N319 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N566 10 KO: K00043, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N542 10 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N337 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N886 10 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N528 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N295 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N966 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N940 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N407 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N481 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N336 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N530 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N567 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N525 10 KO: K00043, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N771 10 KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N644 10 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N560 10 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N595 10 KO: K00156, KO: K00158, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N349 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N531 10 KO: K00004, KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N568 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N707 10 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N366 10 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N797 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N791 10 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N375 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N387 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N346 10 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N342 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N834 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N314 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N332 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N352 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N367 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N333 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N519 10 KO: K00004, KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N353 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N680 10 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K01905, KO: K03778 N283 10 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N264 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N281 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N821 10 KO: K00156, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N273 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N260 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N817 10 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N438 10 KO: K00116, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01734, KO: K03778 N263 10 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N261 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N313 10 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N401 10 KO: K00102, KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K04020 N584 10 KO: K00102, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N286 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N426 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N362 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N270 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N716 9 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N277 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N614 9 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N423 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N311 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N546 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1073 9 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N635 9 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N492 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N770 9 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N422 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N882 9 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K04020 N427 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N700 9 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1030 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N450 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N322 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N308 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N549 9 KO: K00004, KO: K00116, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N404 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1070 9 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734 N601 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N954 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N699 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N884 9 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N309 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N488 9 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N496 9 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N364 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N502 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N297 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N618 9 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N310 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N526 9 KO: K00004, KO: K00116, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N1083 9 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N749 9 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K04020 N608 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N555 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N955 9 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N454 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N622 9 KO: K00004, KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N477 9 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N497 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N325 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N285 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N534 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N896 9 KO: K00116, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01734 N1008 9 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01659, KO: K01734, KO: K03778, KO: K04020 N465 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N328 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N646 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N449 9 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N320 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N445 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1097 9 KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N384 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N898 9 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N406 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N536 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N321 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N563 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N965 9 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N278 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N734 9 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K04020 N453 9 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N868 9 KO: K00102, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K01905, KO: K03778 N870 9 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N442 9 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N323 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N494 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N447 9 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N591 9 KO: K00004, KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N327 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N417 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N607 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N921 9 KO: K00102, KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K13923 N556 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N482 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N267 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N602 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N385 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N294 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N474 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N572 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N663 9 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N799 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N413 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N394 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N392 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N393 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N371 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N395 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N391 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N372 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N370 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N389 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N369 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N388 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N355 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N379 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N356 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N397 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N331 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N358 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N374 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N378 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N343 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N377 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N341 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N344 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N348 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N575 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N340 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N347 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N373 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N376 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N359 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N357 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N302 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N284 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N334 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N576 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N304 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N291 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N290 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N339 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N396 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N316 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N301 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N289 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N440 9 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N300 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N330 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N360 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N778 9 KO: K00102, KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K13923 N303 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N315 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N398 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N432 9 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N431 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N667 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N439 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N312 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N317 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N793 9 KO: K00116, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01505, KO: K01734 N305 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N380 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N293 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N272 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N399 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N823 9 KO: K00156, KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N279 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N824 9 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K04020 N789 9 KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N414 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N435 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N402 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N459 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N460 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N433 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N403 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N458 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N517 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N682 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N434 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N415 9 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N609 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N639 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N569 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N466 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1025 8 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N768 8 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N636 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N726 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N698 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N691 8 KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N869 8 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N605 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N630 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N718 8 KO: K00156, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N448 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N418 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N919 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N714 8 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N479 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N561 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N411 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N865 8 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N499 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N909 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N543 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N759 8 KO: K00004, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N761 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1018 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778 N456 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N735 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N928 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778 N495 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N500 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N480 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N478 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N701 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N547 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N945 8 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N762 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N493 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N739 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N912 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N484 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N720 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1014 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N744 8 KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N451 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N565 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N498 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N483 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N628 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N889 8 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N624 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N731 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1038 8 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N727 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N615 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N697 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N538 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N688 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1037 8 KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N541 8 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N721 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N971 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1096 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N629 8 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N504 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N587 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N476 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N564 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N746 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N490 8 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N767 8 KO: K00102, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N693 8 KO: K00004, KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N559 8 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N712 8 KO: K00102, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N467 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N711 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N938 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N405 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N524 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N593 8 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N941 8 KO: K00102, KO: K00156, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1056 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N752 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1019 8 KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N503 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N455 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N485 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1042 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N684 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N876 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N657 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N658 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N678 8 KO: K00156, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N792 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N661 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N462 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N672 8 KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N664 8 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N656 8 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N655 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N844 8 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K04020 N674 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N784 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N675 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N463 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N830 8 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N659 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N839 8 KO: K00102, KO: K00156, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N833 8 KO: K00102, KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N782 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N509 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N579 8 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N795 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N430 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N416 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N794 8 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N651 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1091 8 KO: K00156, KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734 N1093 8 KO: K00156, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N437 8 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N582 8 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N683 8 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N989 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N621 7 KO: K00043, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N627 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1055 7 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N922 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N469 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N935 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1013 7 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N1021 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N958 7 KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N907 7 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N937 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N604 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N961 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N634 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1085 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N900 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N592 7 KO: K00627, KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N452 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1045 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N960 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N979 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N748 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N702 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N972 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N906 7 KO: K00102, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N892 7 KO: K00043, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N745 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N598 7 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N725 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N957 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N527 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1028 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1033 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N715 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N428 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N872 7 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N686 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N446 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N687 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N638 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1065 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1011 7 KO: K00656, KO: K01067, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K07246 N733 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1002 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1076 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01734, KO: K03417, KO: K07246 N952 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1032 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N708 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N743 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1060 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N487 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N632 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N980 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N871 7 KO: K00656, KO: K01067, KO: K01442, KO: K01659, KO: K01734, KO: K03778, KO: K07246 N890 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N974 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1022 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N867 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N758 7 KO: K00634, KO: K00656, KO: K01067, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N924 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N981 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N473 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1044 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N723 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N611 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N875 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734 N1005 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N975 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N992 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N936 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N933 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N913 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01734, KO: K03417, KO: K07246 N994 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N685 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1054 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N997 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N760 7 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N532 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1039 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01659, KO: K01734 N1041 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N988 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N944 7 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N585 7 KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734 N754 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N959 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N696 7 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N887 7 KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N550 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1050 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1051 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01659, KO: K01734, KO: K03778 N973 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01659, KO: K01734, KO: K03778 N475 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N486 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N910 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N421 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1068 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1000 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1052 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N741 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N491 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1040 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N948 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N540 7 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N903 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N888 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N468 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N695 7 KO: K00116, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N976 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1012 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N719 7 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N507 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N895 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N692 7 KO: K00634, KO: K00656, KO: K01067, KO: K01442, KO: K01734, KO: K03778, KO: K07246 N894 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N995 7 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N613 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N877 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N617 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N722 7 KO: K00116, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1035 7 KO: K00158, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366, KO: K03778 N649 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N679 7 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03417, KO: K03778, KO: K07246 N677 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N803 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N660 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N787 7 KO: K00627, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N807 7 KO: K00043, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N804 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N800 7 KO: K00156, KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N788 7 KO: K00116, KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01734, KO: K10783 N785 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N854 7 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N843 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N846 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N855 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01659, KO: K01734, KO: K03778 N654 7 KO: K00116, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N842 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N838 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N783 7 KO: K00156, KO: K00656, KO: K01067, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N796 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N836 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N670 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N837 7 KO: K00163, KO: K00627, KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N520 7 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N669 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N835 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N671 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N840 7 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N829 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N819 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N518 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N580 7 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N668 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N780 7 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N831 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N577 7 KO: K00627, KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N832 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N798 7 KO: K00634, KO: K00656, KO: K00929, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N815 7 KO: K00102, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N820 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N826 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N441 7 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778 N583 7 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778 N464 7 KO: K00634, KO: K00656, KO: K00929, KO: K01067, KO: K01442, KO: K01734, KO: K03778 N461 7 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N848 7 KO: K00156, KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N513 7 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N511 7 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N596 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N537 6 KO: K00102, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N732 6 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N506 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1015 6 KO: K00158, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N606 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N943 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N946 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734 N915 6 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N1059 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N923 6 KO: K00158, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03366 N1001 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1064 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N706 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N642 6 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N764 6 KO: K00158, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N874 6 KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N600 6 KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N710 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N993 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N523 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N626 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1043 6 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N557 6 KO: K00102, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N916 6 KO: K00656, KO: K01069, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N1077 6 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N978 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N990 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N553 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1082 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01659, KO: K01734 N529 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N544 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N902 6 KO: K00043, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1027 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N694 6 KO: K00043, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1029 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1084 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N931 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1075 6 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01734, KO: K03366 N551 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1087 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1010 6 KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N724 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N769 6 KO: K00102, KO: K00656, KO: K01069, KO: K01659, KO: K01734, KO: K03778 N705 6 KO: K00158, KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N603 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N740 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N950 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N420 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1053 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N977 6 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N594 6 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778, KO: K10783 N1080 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N953 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N425 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N472 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N878 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N753 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N766 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N873 6 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N1023 6 KO: K00627, KO: K00656, KO: K01442, KO: K01734, KO: K03366, KO: K03778 N967 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N956 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N1031 6 KO: K00163, KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N985 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N814 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N812 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N662 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N809 6 KO: K00656, KO: K01069, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N858 6 KO: K00043, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N508 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N681 6 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N845 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N673 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N521 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1095 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N581 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N827 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N570 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N571 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N574 6 KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N779 6 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N578 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N457 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N652 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N828 6 KO: K00158, KO: K00627, KO: K00634, KO: K00656, KO: K01442, KO: K01734 N514 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N653 6 KO: K00043, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N849 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N436 6 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N853 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N786 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N512 6 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N510 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N861 6 KO: K00634, KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N647 6 KO: K00656, KO: K01069, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1071 5 KO: K00043, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N932 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N750 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N893 5 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N897 5 KO: K00043, KO: K00627, KO: K00656, KO: K01442, KO: K01734 N729 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1003 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1069 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N616 5 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N964 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N920 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1061 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N738 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N983 5 KO: K00627, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N757 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N755 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1004 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N879 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N962 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N1016 5 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01734 N533 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N645 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N736 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N713 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1006 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N925 5 KO: K00158, KO: K00627, KO: K00656, KO: K01442, KO: K01734 N620 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N880 5 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N747 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N885 5 KO: K00043, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N737 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N554 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N951 5 KO: K00102, KO: K00656, KO: K01069, KO: K01734, KO: K03778 N690 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N730 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N999 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N589 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N545 5 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N763 5 KO: K00656, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N1067 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N703 5 KO: K00656, KO: K01659, KO: K01734, KO: K03778, KO: K10783 N773 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N756 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K10783 N1062 5 KO: K00634, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N1046 5 KO: K00627, KO: K00656, KO: K01442, KO: K01734, KO: K03366 N742 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N704 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N751 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N939 5 KO: K00627, KO: K00656, KO: K01069, KO: K01734, KO: K03778 N984 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N599 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N1066 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N689 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K10783 N562 5 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N918 5 KO: K00656, KO: K01069, KO: K01734, KO: K03778, KO: K10783 N1078 5 KO: K00158, KO: K00627, KO: K00656, KO: K01069, KO: K01734 N1007 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N637 5 KO: K00634, KO: K00656, KO: K01442, KO: K01659, KO: K01734 N859 5 KO: K00102, KO: K00656, KO: K01069, KO: K01734, KO: K03778 N676 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N856 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N665 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N775 5 KO: K00634, KO: K00656, KO: K01442, KO: K01734, KO: K03778 N857 5 KO: K00656, KO: K01069, KO: K01734, KO: K03778, KO: K10783 N802 5 KO: K00043, KO: K00627, KO: K00656, KO: K01442, KO: K01734 N801 5 KO: K00627, KO: K00656, KO: K01069, KO: K01442, KO: K01734 N774 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N847 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N648 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N862 5 KO: K00656, KO: K01069, KO: K01442, KO: K01734, KO: K03778 N852 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N841 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N860 5 KO: K00627, KO: K00656, KO: K01069, KO: K01734, KO: K03778 N864 5 KO: K00656, KO: K00929, KO: K01442, KO: K01734, KO: K03778 N863 5 KO: K00656, KO: K01442, KO: K01659, KO: K01734, KO: K03778 N709 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N982 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N949 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N986 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1047 4 KO: K00656, KO: K01659, KO: K01734, KO: K03778 N1086 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N1017 4 KO: K00656, KO: K01067, KO: K01442, KO: K01734 N899 4 KO: K00116, KO: K00656, KO: K01442, KO: K01734 N927 4 KO: K00656, KO: K01067, KO: K01442, KO: K01734 N969 4 KO: K00116, KO: K00656, KO: K01069, KO: K01734 N772 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N991 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1079 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N1058 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N987 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N1063 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N1049 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N728 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N1009 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1098 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N947 4 KO: K00627, KO: K00656, KO: K01442, KO: K01734 N883 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N934 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N905 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N963 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1034 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N998 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N929 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N881 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N765 4 KO: K00634, KO: K00656, KO: K01442, KO: K01734 N1081 4 KO: K00656, KO: K01442, KO: K01659, KO: K01734 N1048 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N970 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N1024 4 KO: K00102, KO: K00656, KO: K01442, KO: K01734 N911 4 KO: K00656, KO: K01069, KO: K01734, KO: K10783 N1026 4 KO: K00627, KO: K00656, KO: K01442, KO: K01734 N942 4 KO: K00102, KO: K00656, KO: K01442, KO: K01734 N813 4 KO: K00656, KO: K01442, KO: K01734, KO: K03778 N811 4 KO: K00116, KO: K00656, KO: K01069, KO: K01734 N810 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N808 4 KO: K00656, KO: K01069, KO: K01734, KO: K10783 N805 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N806 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N1088 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N781 4 KO: K00656, KO: K01069, KO: K01442, KO: K01734 N776 4 KO: K00116, KO: K00656, KO: K01442, KO: K01734 N1020 3 KO: K00656, KO: K01442, KO: K01734 N930 3 KO: K00656, KO: K01442, KO: K01734 N996 3 KO: K00656, KO: K01442, KO: K01734 N1057 3 KO: K00656, KO: K01442, KO: K01734 N1089 3 KO: K00656, KO: K01659, KO: K01734 N1094 3 KO: K00627, KO: K00656, KO: K03778 N850 3 KO: K00656, KO: K01734, KO: K03778 N1090 2 KO: K00656, KO: K01442 N1092 2 KO: K01442, KO: K01734 N412 0 N287 0

KEGG Orthology Pathway (KO) characterization and F-score of computationally determined network ecologies reported in Table 8 that represent states of health for multiple disease indications.

TABLE 19 KEGG KEGG KEGG annotation annotation number level 1 level 2 KEGG annotation level 3 Full KEGG annotation level 4 KO:K01442 Metabolism Lipid 00121 Secondary bile acid E3.5.1.24; choloylglycine metabolism biosynthesis [PATH:ko00121] hydrolase [EC:3.5.1.24] KO:K00004 Metabolism Carbohydrate 00650 Butanoate metabolism BDH, butB; (R,R)-butanediol metabolism [PATH:ko00650] dehydrogenase/diacetyl reductase [EC:1.1.1.4 1.1.1.303] KO:K00023 Metabolism Carbohydrate 00650 Butanoate metabolism E1.1.1.36, phbB; acetoacetyl-CoA metabolism [PATH:ko00650] reductase [EC:1.1.1.36] KO:K00043 Metabolism Carbohydrate 00650 Butanoate metabolism E1.1.1.61; 4-hydroxybutyrate metabolism [PATH:ko00650] dehydrogenase [EC:1.1.1.61] KO:K00101 Metabolism Carbohydrate 00620 Pyruvate metabolism E1.1.2.3, lldD; L-lactate metabolism [PATH:ko00620] dehydrogenase (cytochrome) [EC:1.1.2.3] KO:K00102 Metabolism Carbohydrate 00620 Pyruvate metabolism E1.1.2.4, dld; D-lactate metabolism [PATH:ko00620] dehydrogenase (cytochrome) [EC:1.1.2.4] KO:K00116 Metabolism Carbohydrate 00620 Pyruvate metabolism mqo; malate dehydrogenase metabolism [PATH:ko00620] (quinone) [EC:1.1.5.4] KO:K00156 Metabolism Carbohydrate 00620 Pyruvate metabolism poxB; pyruvate dehydrogenase metabolism [PATH:ko00620] (quinone) [EC:1.2.5.1] KO:K00158 Metabolism Carbohydrate 00620 Pyruvate metabolism E1.2.3.3, poxL; pyruvate oxidase metabolism [PATH:ko00620] [EC:1.2.3.3] KO:K00163 Metabolism Carbohydrate 00650 Butanoate metabolism aceE; pyruvate dehydrogenase E1 metabolism [PATH:ko00650] component [EC:1.2.4.1] KO:K00627 Metabolism Carbohydrate 00620 Pyruvate metabolism DLAT, aceF, pdhC; pyruvate metabolism [PATH:ko00620] dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC:2.3.1.12] KO:K00634 Metabolism Carbohydrate 00650 Butanoate metabolism ptb; phosphate butyryltransferase metabolism [PATH:ko00650] [EC:2.3.1.19] KO:K00656 Metabolism Carbohydrate 00650 Butanoate metabolism E2.3.1.54, pflD; formate C- metabolism [PATH:ko00650] acetyltransferase [EC:2.3.1.54] KO:K00929 Metabolism Carbohydrate 00650 Butanoate metabolism E2.7.2.7, buk; butyrate kinase metabolism [PATH:ko00650] [EC:2.7.2.7] KO:K00932 Metabolism Carbohydrate 00640 Propanoate metabolism E2.7.2.15, tdcD, pduW; propionate metabolism [PATH:ko00640] kinase [EC:2.7.2.15] KO:K01067 Metabolism Carbohydrate 00620 Pyruvate metabolism E3.1.2.1, ACH1; acetyl-CoA metabolism [PATH:ko00620] hydrolase [EC:3.1.2.1] KO:K01069 Metabolism Carbohydrate 00620 Pyruvate metabolism E3.1.2.6, gloB; metabolism [PATH:ko00620] hydroxyacylglutathione hydrolase [EC:3.1.2.6] KO:K01505 Metabolism Carbohydrate 00640 Propanoate metabolism E3.5.99.7; 1-aminocyclopropane-1- metabolism [PATH:ko00640] carboxylate deaminase [EC:3.5.99.7] KO:K01659 Metabolism Carbohydrate 00640 Propanoate metabolism E2.3.3.5, pipC; 2-methylcitrate metabolism [PATH:ko00640] synthase [EC:2.3.3.5] KO:K01720 Metabolism Carbohydrate 00640 Propanoate metabolism E4.2.1.79, pipD; 2-methylcitrate metabolism [PATH:ko00640] dehydratase [EC:4.2.1.79] KO:K01734 Metabolism Carbohydrate 00620 Pyruvate metabolism E4.2.3.3, mgsA; methylglyoxal metabolism [PATH:ko00620] synthase [EC:4.2.3.3] KO:K01896 Metabolism Carbohydrate 00650 Butanoate metabolism ACSM; medium-chain acyl-CoA metabolism [PATH:ko00650] synthetase [EC:6.2.1.2] KO:K01905 Metabolism Carbohydrate 00640 Propanoate metabolism E6.2.1.13; acetyl-CoA synthetase metabolism [PATH:ko00640] (ADP-forming) [EC:6.2.1.13] KO:K01907 Metabolism Carbohydrate 00650 Butanoate metabolism AACS, acsA; acetoacetyl-CoA metabolism [PATH:ko00650] synthetase [EC:6.2.1.16] KO:K01908 Metabolism Carbohydrate 00640 Propanoate metabolism E6.2.1.17, pipE; propionyl-CoA metabolism [PATH:ko00640] synthetase [EC:6.2.1.17] KO:K03366 Metabolism Carbohydrate 00650 Butanoate metabolism butA; (R,R)-butanediol metabolism [PATH:ko00650] dehydrogenase/diacetyl reductase [EC:1.1.1.4 1.1.1.303] KO:K03416 Metabolism Carbohydrate 00640 Propanoate metabolism E2.1.3.1; methylmalonyl-CoA metabolism [PATH:ko00640] carboxyltransferase [EC:2.1.3.1] KO:K03417 Metabolism Carbohydrate 00640 Propanoate metabolism E4.1.3.30, pipB; methylisocitrate metabolism [PATH:ko00640] lyase [EC:4.1.3.30] KO:K03777 Metabolism Carbohydrate 00620 Pyruvate metabolism dld; D-lactate dehydrogenase metabolism [PATH:ko00620] [EC:1.1.1.28] KO:K03778 Metabolism Carbohydrate 00620 Pyruvate metabolism ldhA; D-lactate dehydrogenase metabolism [PATH:ko00620] [EC:1.1.1.28] KO:K03821 Metabolism Carbohydrate 00650 Butanoate metabolism phbC, phaC; polyhydroxyalkanoate metabolism [PATH:ko00650] synthase [EC:2.3.1.-] KO:K04020 Metabolism Carbohydrate 00620 Pyruvate metabolism eutD; phosphotransacetylase metabolism [PATH:ko00620] KO:K05973 Metabolism Carbohydrate 00650 Butanoate metabolism E3.1.1.75, phaZ; poly(3- metabolism [PATH:ko00650] hydroxybutyrate) depolymerase [EC:3.1.1.75] KO:K07246 Metabolism Carbohydrate 00650 Butanoate metabolism ttuC, dmlA; tartrate metabolism [PATH:ko00650] dehydrogenase/decarboxylase/D- malate dehydrogenase [EC:1.1.1.934.1.1.73 1.1.1.83] KO:K10783 Metabolism Carbohydrate 00650 Butanoate metabolism E1.3.1.44; trans-2-enoyl-CoA metabolism [PATH:ko00650] reductase (NAD+) [EC:1.3.1.44] KO:K13923 Metabolism Carbohydrate 00640 Propanoate metabolism pduL; phosphotransacylase metabolism [PATH:ko00640]

KEGG Orthology Pathway (KO) hierarchical ontology for KOs identified in computationally determined networks characteristic of states of health and reported in Table 18.

TABLE 20 OTU-1 is a OTU-2 C. diff Key- is a Key- Inhibition OTU-1 stone OTU-2 Stone Score Bacteroides_caccae 1 Bacteroides_eggerthii ++++ Bacteroides_sp_D20 1 Bacteroides_eggerthii Clostridium_nexile 1 Bacteroides_eggerthii Coprococcus_catus 1 Bacteroides_eggerthii + Dorea_formicigenerans 1 Bacteroides_eggerthii Dorea_longicatena 1 Bacteroides_eggerthii − Faecalibacterium_prausnitzii 1 Bacteroides_eggerthii Odoribacter_splanchnicus 1 Bacteroides_eggerthii Parabacteroides_merdae 1 Bacteroides_eggerthii Roseburia_intestinalis 1 Bacteroides_eggerthii Ruminococcus_obeum 1 Bacteroides_eggerthii ++++ Bacteroides_caccae 1 Bifidobacterium_adolescentis ++++ Bacteroides_sp_D20 1 Bifidobacterium_adolescentis ++++ Clostridium_nexile 1 Bifidobacterium_adolescentis ++++ Coprococcus_catus 1 Bifidobacterium_adolescentis Dorea_formicigenerans 1 Bifidobacterium_adolescentis ++++ Dorea_longicatena 1 Bifidobacterium_adolescentis ++++ Faecalibacterium_prausnitzii 1 Bifidobacterium_adolescentis + Odoribacter_splanchnicus 1 Bifidobacterium_adolescentis +++ Parabacteroides_merdae 1 Bifidobacterium_adolescentis ++++ Roseburia_intestinalis 1 Bifidobacterium_adolescentis +++ Ruminococcus_obeum 1 Bifidobacterium_adolescentis ++++ Ruminococcus_torques 1 Bifidobacterium_adolescentis ++++ Bacteroides_caccae 1 Bifidobacterium_pseudocatenulatum ++++ Bacteroides_sp_D20 1 Bifidobacterium_pseudocatenulatum −− Clostridium_nexile 1 Bifidobacterium_pseudocatenulatum ++++ Coprococcus_catus 1 Bifidobacterium_pseudocatenulatum Dorea_formicigenerans 1 Bifidobacterium_pseudocatenulatum +++ Dorea_longicatena 1 Bifidobacterium_pseudocatenulatum ++++ Faecalibacterium_prausnitzii 1 Bifidobacterium_pseudocatenulatum ++ Odoribacter_splanchnicus 1 Bifidobacterium_pseudocatenulatum + Parabacteroides_merdae 1 Bifidobacterium_pseudocatenulatum ++++ Roseburia_intestinalis 1 Bifidobacterium_pseudocatenulatum +++ Ruminococcus_obeum 1 Bifidobacterium_pseudocatenulatum ++++ Ruminococcus_torques 1 Bifidobacterium_pseudocatenulatum ++++ Bacteroides_caccae 1 Blautia_schinkii Bacteroides_sp_D20 1 Blautia_schinkii −− Clostridium_nexile 1 Blautia_schinkii −− Coprococcus_catus 1 Blautia_schinkii −−− Coprococcus_comes 1 Blautia_schinkii + Dorea_formicigenerans 1 Blautia_schinkii Dorea_longicatena 1 Blautia_schinkii +++ Eubacterium_rectale 1 Blautia_schinkii + Faecalibacterium_prausnitzii 1 Blautia_schinkii Faecalibacterium_prausnitzii 1 Blautia_schinkii Odoribacter_splanchnicus 1 Blautia_schinkii − Odoribacter_splanchnicus 1 Blautia_schinkii Parabacteroides_merdae 1 Blautia_schinkii Roseburia_intestinalis 1 Blautia_schinkii − Ruminococcus_obeum 1 Blautia_schinkii Ruminococcus_torques 1 Blautia_schinkii Coprococcus_comes 1 Clostridium_butyricum ++++ Coprococcus_comes 1 Clostridium_orbiscindens ++++ Faecalibacterium_prausnitzii 1 Clostridium_orbiscindens Coprococcus_comes 1 Clostridium_bolteae ++++ Coprococcus_comes 1 Clostridium_hylemonae + Clostridium_nexile 1 Clostridium_sp_HGF2 ++++ Dorea_formicigenerans 1 Clostridium_sp_HGF2 Clostridium_nexile 1 Erysipelotrichaceae_bacterium Coprococcus_catus 1 Erysipelotrichaceae_bacterium Dorea_formicigenerans 1 Erysipelotrichaceae_bacterium −− Dorea_longicatena 1 Erysipelotrichaceae_bacterium Faecalibacterium_prausnitzii 1 Erysipelotrichaceae_bacterium − Odoribacter_splanchnicus 1 Erysipelotrichaceae_bacterium Roseburia_intestinalis 1 Erysipelotrichaceae_bacterium − Bacteroides_caccae 1 Lachnospiraceae_bacterium_5_1_57FAA Bacteroides_sp_D20 1 Lachnospiraceae_bacterium_5_1_57FAA −−− Clostridium_nexile 1 Lachnospiraceae_bacterium_5_1_57FAA − Coprococcus_catus 1 Lachnospiraceae_bacterium_5_1_57FAA Coprococcus_comes 1 Lachnospiraceae_bacterium_5_1_57FAA Coprococcus_comes 1 Lachnospiraceae_bacterium_5_1_57FAA ++++ Dorea_formicigenerans 1 Lachnospiraceae_bacterium_5_1_57FAA −− Dorea_longicatena 1 Lachnospiraceae_bacterium_5_1_57FAA ++++ Eubacterium_rectale 1 Lachnospiraceae_bacterium_5_1_57FAA Faecalibacterium_prausnitzii 1 Lachnospiraceae_bacterium_5_1_57FAA Faecalibacterium_prausnitzii 1 Lachnospiraceae_bacterium_5_1_57FAA Faecalibacterium_prausnitzii 1 Lachnospiraceae_bacterium_5_1_57FAA ++++ Odoribacter_splanchnicus 1 Lachnospiraceae_bacterium_5_1_57FAA −− Odoribacter_splanchnicus 1 Lachnospiraceae_bacterium_5_1_57FAA Parabacteroides_merdae 1 Lachnospiraceae_bacterium_5_1_57FAA − Roseburia_intestinalis 1 Lachnospiraceae_bacterium_5_1_57FAA Ruminococcus_obeum 1 Lachnospiraceae_bacterium_5_1_57FAA Ruminococcus_torques 1 Lachnospiraceae_bacterium_5_1_57FAA Bacteroides_eggerthii Alistipes_shahii 1 −− Bacteroides_sp_1_1_6 Alistipes_shahii 1 ++++ Bacteroides_sp_3_1_23 Alistipes_shahii 1 + Bifidobacterium_adolescentis Alistipes_shahii 1 ++++ Bifidobacterium_pseudocatenulatum Alistipes_shahii 1 Blautia_schinkii Alistipes_shahii 1 Clostridium_sp_HGF2 Alistipes_shahii 1 Coprobacillus_sp_D7 Alistipes_shahii 1 ++++ Enterococcus_faecalis Alistipes_shahii 1 ++++ Erysipelotrichaceae_bacterium Alistipes_shahii 1 −−− Lachnospiraceae_bacterium_5_1_57FAA Alistipes_shahii 1 Bacteroides_sp_1_1_6 Bacteroides_caccae 1 ++++ Bacteroides_sp_3_1_23 Bacteroides_caccae 1 +++ Clostridium_sp_HGF2 Bacteroides_caccae 1 Coprobacillus_sp_D7 Bacteroides_caccae 1 +++ Enterococcus_faecalis Bacteroides_caccae 1 ++++ Erysipelotrichaceae_bacterium Bacteroides_caccae 1 ++ Bacteroides_sp_1_1_6 Bacteroides_sp_D20 1 ++++ Bacteroides_sp_3_1_23 Bacteroides_sp_D20 1 ++++ Clostridium_sp_HGF2 Bacteroides_sp_D20 1 Coprobacillus_sp_D7 Bacteroides_sp_D20 1 Enterococcus_faecalis Bacteroides_sp_D20 1 ++++ Erysipelotrichaceae_bacterium Bacteroides_sp_D20 1 Bacteroides_sp_1_1_6 Clostridium_nexile 1 ++++ Bacteroides_sp_3_1_23 Clostridium_nexile 1 ++++ Coprobacillus_sp_D7 Clostridium_nexile 1 Enterococcus_faecalis Clostridium_nexile 1 ++++ Bacteroides_sp_1_1_6 Coprococcus_catus 1 ++++ Bacteroides_sp_3_1_23 Coprococcus_catus 1 Clostridium_sp_HGF2 Coprococcus_catus 1 −−− Coprobacillus_sp_D7 Coprococcus_catus 1 −−− Enterococcus_faecalis Coprococcus_catus 1 ++++ Bacteroides_eggerthii Coprococcus_comes 1 +++ Bacteroides_sp_1_1_6 Coprococcus_comes 1 +++ Bacteroides_sp_3_1_23 Coprococcus_comes 1 ++++ Bifidobacterium_adolescentis Coprococcus_comes 1 ++++ Bifidobacterium_pseudocatenulatum Coprococcus_comes 1 ++++ Clostridium_butyricum Coprococcus_comes 1 ++++ Clostridium_disporicum Coprococcus_comes 1 ++++ Clostridium_hylemonae Coprococcus_comes 1 + Clostridium_innocuum Coprococcus_comes 1 ++++ Clostridium_mayombei Coprococcus_comes 1 ++++ Clostridium_sp_HGF2 Coprococcus_comes 1 Clostridium_tertium Coprococcus_comes 1 ++++ Coprobacillus_sp_D7 Coprococcus_comes 1 +++ Enterococcus_faecalis Coprococcus_comes 1 ++++ Erysipelotrichaceae_bacterium Coprococcus_comes 1 − Bacteroides_sp_1_1_6 Dorea_formicigenerans 1 +++ Bacteroides_sp_3_1_23 Dorea_formicigenerans 1 Coprobacillus_sp_D7 Dorea_formicigenerans 1 − Enterococcus_faecalis Dorea_formicigenerans 1 ++++ Bacteroides_sp_1_1_6 Dorea_longicatena 1 ++++ Bacteroides_sp_3_1_23 Dorea_longicatena 1 +++ Clostridium_sp_HGF2 Dorea_longicatena 1 −− Coprobacillus_sp_D7 Dorea_longicatena 1 Enterococcus_faecalis Dorea_longicatena 1 ++++ Bacteroides_eggerthii Eubacterium_rectale 1 Bacteroides_sp_1_1_6 Eubacterium_rectale 1 ++++ Bacteroides_sp_3_1_23 Eubacterium_rectale 1 +++ Bifidobacterium_adolescentis Eubacterium_rectale 1 ++++ Bifidobacterium_pseudocatenulatum Eubacterium_rectale 1 Clostridium_butyricum Eubacterium_rectale 1 ++++ Clostridium_orbiscindens Eubacterium_rectale 1 + Clostridium_bolteae Eubacterium_rectale 1 ++ Clostridium_disporicum Eubacterium_rectale 1 ++++ Clostridium_hylemonae Eubacterium_rectale 1 Clostridium_innocuum Eubacterium_rectale 1 ++++ Clostridium_mayombei Eubacterium_rectale 1 ++++ Clostridium_sp_HGF2 Eubacterium_rectale 1 −− Clostridium_tertium Eubacterium_rectale 1 ++++ Coprobacillus_sp_D7 Eubacterium_rectale 1 +++ Enterococcus_faecalis Eubacterium_rectale 1 ++++ Erysipelotrichaceae_bacterium Eubacterium_rectale 1 − Lachnospiraceae_bacterium_5_1_57FAA Eubacterium_rectale 1 +++ Bacteroides_eggerthii Faecalibacterium_prausnitzii 1 − Bacteroides_sp_1_1_6 Faecalibacterium_prausnitzii 1 ++++ Bacteroides_sp_1_1_6 Faecalibacterium_prausnitzii 1 +++ Bacteroides_sp_3_1_23 Faecalibacterium_prausnitzii 1 ++ Bacteroides_sp_3_1_23 Faecalibacterium_prausnitzii 1 Bifidobacterium_adolescentis Faecalibacterium_prausnitzii 1 + Bifidobacterium_pseudocatenulatum Faecalibacterium_prausnitzii 1 Clostridium_butyricum Faecalibacterium_prausnitzii 1 ++++ Clostridium_orbiscindens Faecalibacterium_prausnitzii 1 Clostridium_bolteae Faecalibacterium_prausnitzii 1 ++ Clostridium_disporicum Faecalibacterium_prausnitzii 1 Clostridium_hylemonae Faecalibacterium_prausnitzii 1 Clostridium_innocuum Faecalibacterium_prausnitzii 1 ++++ Clostridium_mayombei Faecalibacterium_prausnitzii 1 ++++ Clostridium_sp_HGF2 Faecalibacterium_prausnitzii 1 ++ Clostridium_sp_HGF2 Faecalibacterium_prausnitzii 1 −− Clostridium_tertium Faecalibacterium_prausnitzii 1 ++++ Coprobacillus_sp_D7 Faecalibacterium_prausnitzii 1 −−− Coprobacillus_sp_D7 Faecalibacterium_prausnitzii 1 Enterococcus_faecalis Faecalibacterium_prausnitzii 1 ++++ Enterococcus_faecalis Faecalibacterium_prausnitzii 1 ++++ Erysipelotrichaceae_bacterium Faecalibacterium_prausnitzii 1 −− Lachnospiraceae_bacterium_5_1_57FAA Faecalibacterium_prausnitzii 1 ++++ Bacteroides_eggerthii Odoribacter_splanchnicus 1 − Bacteroides_sp_1_1_6 Odoribacter_splanchnicus 1 ++++ Bacteroides_sp_1_1_6 Odoribacter_splanchnicus 1 + Bacteroides_sp_3_1_23 Odoribacter_splanchnicus 1 + Bacteroides_sp_3_1_23 Odoribacter_splanchnicus 1 Bifidobacterium_adolescentis Odoribacter_splanchnicus 1 ++++ Bifidobacterium_pseudocatenulatum Odoribacter_splanchnicus 1 +++ Clostridium_sp_HGF2 Odoribacter_splanchnicus 1 Clostridium_sp_HGF2 Odoribacter_splanchnicus 1 −−− Coprobacillus_sp_D7 Odoribacter_splanchnicus 1 − Coprobacillus_sp_D7 Odoribacter_splanchnicus 1 +++ Enterococcus_faecalis Odoribacter_splanchnicus 1 ++++ Enterococcus_faecalis Odoribacter_splanchnicus 1 ++++ Erysipelotrichaceae_bacterium Odoribacter_splanchnicus 1 −− Bacteroides_sp_1_1_6 Parabacteroides_merdae 1 ++++ Bacteroides_sp_3_1_23 Parabacteroides_merdae 1 +++ Clostridium_sp_HGF2 Parabacteroides_merdae 1 +++ Coprobacillus_sp_D7 Parabacteroides_merdae 1 − Enterococcus_faecalis Parabacteroides_merdae 1 ++++ Erysipelotrichaceae_bacterium Parabacteroides_merdae 1 Bacteroides_sp_1_1_6 Roseburia_intestinalis 1 ++++ Bacteroides_sp_3_1_23 Roseburia_intestinalis 1 + Clostridium_sp_HGF2 Roseburia_intestinalis 1 −−− Coprobacillus_sp_D7 Roseburia_intestinalis 1 − Enterococcus_faecalis Roseburia_intestinalis 1 ++++ Clostridium_butyricum Ruminococcus_bromii 1 ++++ Clostridium_orbiscindens Ruminococcus_bromii 1 Clostridium_bolteae Ruminococcus_bromii 1 +++ Clostridium_disporicum Ruminococcus_bromii 1 Clostridium_hylemonae Ruminococcus_bromii 1 Clostridium_innocuum Ruminococcus_bromii 1 ++++ Clostridium_mayombei Ruminococcus_bromii 1 ++++ Clostridium_tertium Ruminococcus_bromii 1 ++++ Lachnospiraceae_bacterium_5_1_57FAA Ruminococcus_bromii 1 ++++ Bacteroides_sp_1_1_6 Ruminococcus_obeum 1 +++ Bacteroides_sp_3_1_23 Ruminococcus_obeum 1 +++ Clostridium_sp_HGF2 Ruminococcus_obeum 1 −− Coprobacillus_sp_D7 Ruminococcus_obeum 1 + Enterococcus_faecalis Ruminococcus_obeum 1 ++++ Erysipelotrichaceae_bacterium Ruminococcus_obeum 1 Bacteroides_eggerthii Ruminococcus_torques 1 ++++ Bacteroides_sp_1_1_6 Ruminococcus_torques 1 ++++ Bacteroides_sp_3_1_23 Ruminococcus_torques 1 ++++ Clostridium_sp_HGF2 Ruminococcus_torques 1 Coprobacillus_sp_D7 Ruminococcus_torques 1 ++++ Enterococcus_faecalis Ruminococcus_torques 1 ++++ Erysipelotrichaceae_bacterium Ruminococcus_torques 1 + Alistipes_shahii 1 Alistipes_shahii 1 Bacteroides_caccae 1 Alistipes_shahii 1 Bacteroides_sp_D20 1 Alistipes_shahii 1 − Clostridium_nexile 1 Alistipes_shahii 1 Coprococcus_catus 1 Alistipes_shahii 1 − Coprococcus_comes 1 Alistipes_shahii 1 Dorea_formicigenerans 1 Alistipes_shahii 1 −−−− Dorea_longicatena 1 Alistipes_shahii 1 ++++ Eubacterium_rectale 1 Alistipes_shahii 1 Faecalibacterium_prausnitzii 1 Alistipes_shahii 1 Faecalibacterium_prausnitzii 1 Alistipes_shahii 1 + Odoribacter_splanchnicus 1 Alistipes_shahii 1 Odoribacter_splanchnicus 1 Alistipes_shahii 1 Parabacteroides_merdae 1 Alistipes_shahii 1 Roseburia_intestinalis 1 Alistipes_shahii 1 − Ruminococcus_obeum 1 Alistipes_shahii 1 Ruminococcus_torques 1 Alistipes_shahii 1 Bacteroides_caccae 1 Bacteroides_caccae 1 ++++ Bacteroides_sp_D20 1 Bacteroides_caccae 1 +++ Clostridium_nexile 1 Bacteroides_caccae 1 Coprococcus_catus 1 Bacteroides_caccae 1 ++++ Dorea_formicigenerans 1 Bacteroides_caccae 1 +++ Dorea_longicatena 1 Bacteroides_caccae 1 Faecalibacterium_prausnitzii 1 Bacteroides_caccae 1 − Odoribacter_splanchnicus 1 Bacteroides_caccae 1 Parabacteroides_merdae 1 Bacteroides_caccae 1 + Roseburia_intestinalis 1 Bacteroides_caccae 1 + Ruminococcus_obeum 1 Bacteroides_caccae 1 ++++ Bacteroides_sp_D20 1 Bacteroides_sp_D20 1 Clostridium_nexile 1 Bacteroides_sp_D20 1 − Coprococcus_catus 1 Bacteroides_sp_D20 1 Dorea_formicigenerans 1 Bacteroides_sp_D20 1 − Dorea_longicatena 1 Bacteroides_sp_D20 1 Faecalibacterium_prausnitzii 1 Bacteroides_sp_D20 1 Odoribacter_splanchnicus 1 Bacteroides_sp_D20 1 Roseburia_intestinalis 1 Bacteroides_sp_D20 1 − Clostridium_nexile 1 Clostridium_nexile 1 ++ Dorea_formicigenerans 1 Clostridium_nexile 1 Clostridium_nexile 1 Coprococcus_catus 1 Coprococcus_catus 1 Coprococcus_catus 1 Dorea_formicigenerans 1 Coprococcus_catus 1 Dorea_longicatena 1 Coprococcus_catus 1 Faecalibacterium_prausnitzii 1 Coprococcus_catus 1 Odoribacter_splanchnicus 1 Coprococcus_catus 1 Roseburia_intestinalis 1 Coprococcus_catus 1 Bacteroides_caccae 1 Coprococcus_comes 1 +++ Bacteroides_sp_D20 1 Coprococcus_comes 1 Clostridium_nexile 1 Coprococcus_comes 1 Coprococcus_catus 1 Coprococcus_comes 1 −− Coprococcus_comes 1 Coprococcus_comes 1 Coprococcus_comes 1 Coprococcus_comes 1 ++ Dorea_formicigenerans 1 Coprococcus_comes 1 Dorea_longicatena 1 Coprococcus_comes 1 Faecalibacterium_prausnitzii 1 Coprococcus_comes 1 Odoribacter_splanchnicus 1 Coprococcus_comes 1 Parabacteroides_merdae 1 Coprococcus_comes 1 − Roseburia_intestinalis 1 Coprococcus_comes 1 − Ruminococcus_obeum 1 Coprococcus_comes 1 ++++ Ruminococcus_torques 1 Coprococcus_comes 1 ++++ Dorea_formicigenerans 1 Dorea_formicigenerans 1 −− Clostridium_nexile 1 Dorea_longicatena 1 Dorea_formicigenerans 1 Dorea_longicatena 1 ++ Dorea_longicatena 1 Dorea_longicatena 1 − Faecalibacterium_prausnitzii 1 Dorea_longicatena 1 − Odoribacter_splanchnicus 1 Dorea_longicatena 1 Bacteroides_caccae 1 Eubacterium_rectale 1 Bacteroides_sp_D20 1 Eubacterium_rectale 1 −− Clostridium_nexile 1 Eubacterium_rectale 1 − Coprococcus_catus 1 Eubacterium_rectale 1 −−− Coprococcus_comes 1 Eubacterium_rectale 1 + Coprococcus_comes 1 Eubacterium_rectale 1 ++++ Dorea_formicigenerans 1 Eubacterium_rectale 1 − Dorea_longicatena 1 Eubacterium_rectale 1 ++++ Eubacterium_rectale 1 Eubacterium_rectale 1 +++ Eubacterium_rectale 1 Eubacterium_rectale 1 Faecalibacterium_prausnitzii 1 Eubacterium_rectale 1 −− Faecalibacterium_prausnitzii 1 Eubacterium_rectale 1 Odoribacter_splanchnicus 1 Eubacterium_rectale 1 − Parabacteroides_merdae 1 Eubacterium_rectale 1 − Roseburia_intestinalis 1 Eubacterium_rectale 1 −−−− Ruminococcus_bromii 1 Eubacterium_rectale 1 + Ruminococcus_obeum 1 Eubacterium_rectale 1 ++ Ruminococcus_torques 1 Eubacterium_rectale 1 + Bacteroides_caccae 1 Faecalibacterium_prausnitzii 1 Bacteroides_sp_D20 1 Faecalibacterium_prausnitzii 1 −− Clostridium_nexile 1 Faecalibacterium_prausnitzii 1 Clostridium_nexile 1 Faecalibacterium_prausnitzii 1 − Coprococcus_catus 1 Faecalibacterium_prausnitzii 1 −−− Coprococcus_comes 1 Faecalibacterium_prausnitzii 1 Coprococcus_comes 1 Faecalibacterium_prausnitzii 1 +++ Dorea_formicigenerans 1 Faecalibacterium_prausnitzii 1 Dorea_formicigenerans 1 Faecalibacterium_prausnitzii 1 −−− Dorea_longicatena 1 Faecalibacterium_prausnitzii 1 +++ Eubacterium_rectale 1 Faecalibacterium_prausnitzii 1 + Faecalibacterium_prausnitzii 1 Faecalibacterium_prausnitzii 1 + Faecalibacterium_prausnitzii 1 Faecalibacterium_prausnitzii 1 Faecalibacterium_prausnitzii 1 Faecalibacterium_prausnitzii 1 + Faecalibacterium_prausnitzii 1 Faecalibacterium_prausnitzii 1 Odoribacter_splanchnicus 1 Faecalibacterium_prausnitzii 1 −− Parabacteroides_merdae 1 Faecalibacterium_prausnitzii 1 − Roseburia_intestinalis 1 Faecalibacterium_prausnitzii 1 Ruminococcus_obeum 1 Faecalibacterium_prausnitzii 1 Ruminococcus_torques 1 Faecalibacterium_prausnitzii 1 Bacteroides_caccae 1 Odoribacter_splanchnicus 1 Bacteroides_sp_D20 1 Odoribacter_splanchnicus 1 −−− Clostridium_nexile 1 Odoribacter_splanchnicus 1 Clostridium_nexile 1 Odoribacter_splanchnicus 1 −−− Coprococcus_catus 1 Odoribacter_splanchnicus 1 −− Coprococcus_comes 1 Odoribacter_splanchnicus 1 Dorea_formicigenerans 1 Odoribacter_splanchnicus 1 Dorea_formicigenerans 1 Odoribacter_splanchnicus 1 − Dorea_longicatena 1 Odoribacter_splanchnicus 1 ++++ Eubacterium_rectale 1 Odoribacter_splanchnicus 1 + Faecalibacterium_prausnitzii 1 Odoribacter_splanchnicus 1 Faecalibacterium_prausnitzii 1 Odoribacter_splanchnicus 1 − Faecalibacterium_prausnitzii 1 Odoribacter_splanchnicus 1 + Odoribacter_splanchnicus 1 Odoribacter_splanchnicus 1 Odoribacter_splanchnicus 1 Odoribacter_splanchnicus 1 −−− Odoribacter_splanchnicus 1 Odoribacter_splanchnicus 1 + Parabacteroides_merdae 1 Odoribacter_splanchnicus 1 Roseburia_intestinalis 1 Odoribacter_splanchnicus 1 Ruminococcus_obeum 1 Odoribacter_splanchnicus 1 + Ruminococcus_torques 1 Odoribacter_splanchnicus 1 Bacteroides_sp_D20 1 Parabacteroides_merdae 1 Clostridium_nexile 1 Parabacteroides_merdae 1 ++ Coprococcus_catus 1 Parabacteroides_merdae 1 +++ Dorea_formicigenerans 1 Parabacteroides_merdae 1 Dorea_longicatena 1 Parabacteroides_merdae 1 Faecalibacterium_prausnitzii 1 Parabacteroides_merdae 1 + Odoribacter_splanchnicus 1 Parabacteroides_merdae 1 Parabacteroides_merdae 1 Parabacteroides_merdae 1 +++ Roseburia_intestinalis 1 Parabacteroides_merdae 1 Clostridium_nexile 1 Roseburia_intestinalis 1 − Dorea_formicigenerans 1 Roseburia_intestinalis 1 Dorea_longicatena 1 Roseburia_intestinalis 1 − Faecalibacterium_prausnitzii 1 Roseburia_intestinalis 1 Odoribacter_splanchnicus 1 Roseburia_intestinalis 1 − Roseburia_intestinalis 1 Roseburia_intestinalis 1 Coprococcus_comes 1 Ruminococcus_bromii 1 ++++ Eubacterium_rectale 1 Ruminococcus_bromii 1 + Faecalibacterium_prausnitzii 1 Ruminococcus_bromii 1 Ruminococcus_bromii 1 Ruminococcus_bromii 1 − Bacteroides_sp_D20 1 Ruminococcus_obeum 1 Clostridium_nexile 1 Ruminococcus_obeum 1 − Coprococcus_catus 1 Ruminococcus_obeum 1 Dorea_formicigenerans 1 Ruminococcus_obeum 1 ++++ Dorea_longicatena 1 Ruminococcus_obeum 1 − Faecalibacterium_prausnitzii 1 Ruminococcus_obeum 1 Odoribacter_splanchnicus 1 Ruminococcus_obeum 1 − Parabacteroides_merdae 1 Ruminococcus_obeum 1 Roseburia_intestinalis 1 Ruminococcus_obeum 1 Ruminococcus_obeum 1 Ruminococcus_obeum 1 ++++ Bacteroides_caccae 1 Ruminococcus_torques 1 ++++ Bacteroides_sp_D20 1 Ruminococcus_torques 1 ++ Clostridium_nexile 1 Ruminococcus_torques 1 + Coprococcus_catus 1 Ruminococcus_torques 1 + Dorea_formicigenerans 1 Ruminococcus_torques 1 ++++ Dorea_longicatena 1 Ruminococcus_torques 1 Faecalibacterium_prausnitzii 1 Ruminococcus_torques 1 Odoribacter_splanchnicus 1 Ruminococcus_torques 1 Parabacteroides_merdae 1 Ruminococcus_torques 1 + Roseburia_intestinalis 1 Ruminococcus_torques 1 + Ruminococcus_obeum 1 Ruminococcus_torques 1 ++++ Ruminococcus_torques 1 Ruminococcus_torques 1 ++++ Bacteroides_ovatus Alistipes_shahii 1 Bacteroides_vulgatus Alistipes_shahii 1 +++ Bacteroides_vulgatus Alistipes_shahii 1 + Blautia_producta Alistipes_shahii 1 ++++ Clostridium_hathewayi Alistipes_shahii 1 ++++ Clostridium_symbiosum Alistipes_shahii 1 Collinsella_aerofaciens Alistipes_shahii 1 ++++ Escherichia_coli Alistipes_shahii 1 ++++ Escherichia_coli Alistipes_shahii 1 ++++ Eubacterium_eligens Alistipes_shahii 1 −− Streptococcus_thermophilus Alistipes_shahii 1 Bacteroides_ovatus Bacteroides_caccae 1 Bacteroides_vulgatus Bacteroides_caccae 1 ++++ Bacteroides_vulgatus Bacteroides_caccae 1 + Blautia_producta Bacteroides_caccae 1 ++++ Collinsella_aerofaciens Bacteroides_caccae 1 ++++ Escherichia_coli Bacteroides_caccae 1 ++++ Escherichia_coli Bacteroides_caccae 1 ++++ Eubacterium_eligens Bacteroides_caccae 1 ++ Streptococcus_thermophilus Bacteroides_caccae 1 ++ Bacteroides_vulgatus Bacteroides_sp_D20 1 + Blautia_producta Bacteroides_sp_D20 1 ++++ Escherichia_coli Bacteroides_sp_D20 1 ++++ Eubacterium_eligens Bacteroides_sp_D20 1 − Streptococcus_thermophilus Bacteroides_sp_D20 1 + Bacteroides_vulgatus Clostridium_nexile 1 ++++ Blautia_producta Clostridium_nexile 1 ++++ Escherichia_coli Clostridium_nexile 1 ++++ Eubacterium_eligens Clostridium_nexile 1 + Streptococcus_thermophilus Clostridium_nexile 1 + Bacteroides_vulgatus Coprococcus_catus 1 + Blautia_producta Coprococcus_catus 1 ++++ Escherichia_coli Coprococcus_catus 1 ++++ Eubacterium_eligens Coprococcus_catus 1 Streptococcus_thermophilus Coprococcus_catus 1 Bacteroides_ovatus Coprococcus_comes 1 Bacteroides_vulgatus Coprococcus_comes 1 ++++ Bacteroides_vulgatus Coprococcus_comes 1 Blautia_producta Coprococcus_comes 1 ++++ Clostridium_hathewayi Coprococcus_comes 1 ++++ Collinsella_aerofaciens Coprococcus_comes 1 ++++ Collinsella_aerofaciens Coprococcus_comes 1 +++ Escherichia_coli Coprococcus_comes 1 ++++ Escherichia_coli Coprococcus_comes 1 ++++ Eubacterium_eligens Coprococcus_comes 1 ++ Streptococcus_thermophilus Coprococcus_comes 1 ++ Bacteroides_vulgatus Dorea_formicigenerans 1 ++ Escherichia_coli Dorea_formicigenerans 1 ++ Streptococcus_thermophilus Dorea_formicigenerans 1 Bacteroides_vulgatus Dorea_longicatena 1 ++++ Blautia_producta Dorea_longicatena 1 ++++ Escherichia_coli Dorea_longicatena 1 ++++ Eubacterium_eligens Dorea_longicatena 1 ++ Streptococcus_thermophilus Dorea_longicatena 1 + Bacteroides_ovatus Eubacterium_rectale 1 Bacteroides_vulgatus Eubacterium_rectale 1 ++++ Bacteroides_vulgatus Eubacterium_rectale 1 Blautia_producta Eubacterium_rectale 1 ++++ Blautia_producta Eubacterium_rectale 1 ++++ Clostridium_hathewayi Eubacterium_rectale 1 ++++ Clostridium_symbiosum Eubacterium_rectale 1 ++ Clostridium_symbiosum Eubacterium_rectale 1 + Collinsella_aerofaciens Eubacterium_rectale 1 ++++ Collinsella_aerofaciens Eubacterium_rectale 1 ++++ Escherichia_coli Eubacterium_rectale 1 ++++ Escherichia_coli Eubacterium_rectale 1 ++++ Eubacterium_eligens Eubacterium_rectale 1 Ruminococcus_gnavus Eubacterium_rectale 1 ++++ Streptococcus_thermophilus Eubacterium_rectale 1 Bacteroides_ovatus Faecalibacterium_prausnitzii 1 − Bacteroides_vulgatus Faecalibacterium_prausnitzii 1 ++++ Bacteroides_vulgatus Faecalibacterium_prausnitzii 1 +++ Bacteroides_vulgatus Faecalibacterium_prausnitzii 1 −−− Blautia_producta Faecalibacterium_prausnitzii 1 ++++ Blautia_producta Faecalibacterium_prausnitzii 1 ++++ Clostridium_hathewayi Faecalibacterium_prausnitzii 1 +++ Clostridium_symbiosum Faecalibacterium_prausnitzii 1 +++ Clostridium_symbiosum Faecalibacterium_prausnitzii 1 ++++ Collinsella_aerofaciens Faecalibacterium_prausnitzii 1 ++++ Collinsella_aerofaciens Faecalibacterium_prausnitzii 1 ++++ Escherichia_coli Faecalibacterium_prausnitzii 1 ++++ Escherichia_coli Faecalibacterium_prausnitzii 1 ++++ Escherichia_coli Faecalibacterium_prausnitzii 1 ++ Eubacterium_eligens Faecalibacterium_prausnitzii 1 Eubacterium_eligens Faecalibacterium_prausnitzii 1 Streptococcus_thermophilus Faecalibacterium_prausnitzii 1 Streptococcus_thermophilus Faecalibacterium_prausnitzii 1 Bacteroides_ovatus Odoribacter_splanchnicus 1 −− Bacteroides_vulgatus Odoribacter_splanchnicus 1 +++ Bacteroides_vulgatus Odoribacter_splanchnicus 1 +++ Bacteroides_vulgatus Odoribacter_splanchnicus 1 − Blautia_producta Odoribacter_splanchnicus 1 ++++ Blautia_producta Odoribacter_splanchnicus 1 ++++ Clostridium_hathewayi Odoribacter_splanchnicus 1 ++++ Clostridium_symbiosum Odoribacter_splanchnicus 1 ++ Collinsella_aerofaciens Odoribacter_splanchnicus 1 ++++ Escherichia_coli Odoribacter_splanchnicus 1 ++++ Escherichia_coli Odoribacter_splanchnicus 1 ++++ Escherichia_coli Odoribacter_splanchnicus 1 ++++ Eubacterium_eligens Odoribacter_splanchnicus 1 Eubacterium_eligens Odoribacter_splanchnicus 1 Streptococcus_thermophilus Odoribacter_splanchnicus 1 Streptococcus_thermophilus Odoribacter_splanchnicus 1 + Bacteroides_ovatus Parabacteroides_merdae 1 Bacteroides_vulgatus Parabacteroides_merdae 1 ++++ Blautia_producta Parabacteroides_merdae 1 ++++ Escherichia_coli Parabacteroides_merdae 1 ++++ Eubacterium_eligens Parabacteroides_merdae 1 Streptococcus_thermophilus Parabacteroides_merdae 1 Bacteroides_vulgatus Roseburia_intestinalis 1 + Blautia_producta Roseburia_intestinalis 1 ++++ Escherichia_coli Roseburia_intestinalis 1 ++++ Eubacterium_eligens Roseburia_intestinalis 1 Streptococcus_thermophilus Roseburia_intestinalis 1 Blautia_producta Ruminococcus_bromii 1 ++++ Clostridium_symbiosum Ruminococcus_bromii 1 ++++ Collinsella_aerofaciens Ruminococcus_bromii 1 ++++ Ruminococcus_gnavus Ruminococcus_bromii 1 ++++ Bacteroides_ovatus Ruminococcus_obeum 1 Bacteroides_vulgatus Ruminococcus_obeum 1 ++++ Bacteroides_vulgatus Ruminococcus_obeum 1 Blautia_producta Ruminococcus_obeum 1 ++++ Collinsella_aerofaciens Ruminococcus_obeum 1 ++++ Escherichia_coli Ruminococcus_obeum 1 +++ Escherichia_coli Ruminococcus_obeum 1 ++++ Eubacterium_eligens Ruminococcus_obeum 1 + Streptococcus_thermophilus Ruminococcus_obeum 1 +++ Bacteroides_ovatus Ruminococcus_torques 1 ++++ Bacteroides_vulgatus Ruminococcus_torques 1 ++++ Bacteroides_vulgatus Ruminococcus_torques 1 ++++ Blautia_producta Ruminococcus_torques 1 ++++ Collinsella_aerofaciens Ruminococcus_torques 1 ++++ Escherichia_coli Ruminococcus_torques 1 ++++ Escherichia_coli Ruminococcus_torques 1 ++++ Eubacterium_eligens Ruminococcus_torques 1 ++ Streptococcus_thermophilus Ruminococcus_torques 1 + Bacteroides_sp_D20 1 Bacteroides_ovatus − Clostridium_nexile 1 Bacteroides_ovatus Coprococcus_catus 1 Bacteroides_ovatus Dorea_formicigenerans 1 Bacteroides_ovatus Dorea_longicatena 1 Bacteroides_ovatus − Faecalibacterium_prausnitzii 1 Bacteroides_ovatus Odoribacter_splanchnicus 1 Bacteroides_ovatus Roseburia_intestinalis 1 Bacteroides_ovatus Bacteroides_sp_D20 1 Bacteroides_vulgatus Clostridium_nexile 1 Bacteroides_vulgatus Coprococcus_catus 1 Bacteroides_vulgatus ++ Dorea_formicigenerans 1 Bacteroides_vulgatus Dorea_longicatena 1 Bacteroides_vulgatus Faecalibacterium_prausnitzii 1 Bacteroides_vulgatus Odoribacter_splanchnicus 1 Bacteroides_vulgatus Parabacteroides_merdae 1 Bacteroides_vulgatus + Roseburia_intestinalis 1 Bacteroides_vulgatus Alistipes_shahii 1 Blautia_producta Bacteroides_caccae 1 Blautia_producta + Bacteroides_sp_D20 1 Blautia_producta Clostridium_nexile 1 Blautia_producta − Coprococcus_catus 1 Blautia_producta −−−− Coprococcus_comes 1 Blautia_producta Coprococcus_comes 1 Blautia_producta ++++ Dorea_formicigenerans 1 Blautia_producta ++++ Dorea_formicigenerans 1 Blautia_producta −− Dorea_longicatena 1 Blautia_producta +++ Eubacterium_rectale 1 Blautia_producta + Faecalibacterium_prausnitzii 1 Blautia_producta Faecalibacterium_prausnitzii 1 Blautia_producta + Faecalibacterium_prausnitzii 1 Blautia_producta ++++ Odoribacter_splanchnicus 1 Blautia_producta − Odoribacter_splanchnicus 1 Blautia_producta + Parabacteroides_merdae 1 Blautia_producta +++ Roseburia_intestinalis 1 Blautia_producta −− Ruminococcus_obeum 1 Blautia_producta Ruminococcus_torques 1 Blautia_producta Bacteroides_caccae 1 Clostridium_hathewayi ++++ Bacteroides_sp_D20 1 Clostridium_hathewayi ++++ Clostridium_nexile 1 Clostridium_hathewayi Coprococcus_catus 1 Clostridium_hathewayi +++ Dorea_formicigenerans 1 Clostridium_hathewayi ++++ Dorea_longicatena 1 Clostridium_hathewayi + Faecalibacterium_prausnitzii 1 Clostridium_hathewayi Odoribacter_splanchnicus 1 Clostridium_hathewayi Parabacteroides_merdae 1 Clostridium_hathewayi + Roseburia_intestinalis 1 Clostridium_hathewayi +++ Ruminococcus_obeum 1 Clostridium_hathewayi ++++ Ruminococcus_torques 1 Clostridium_hathewayi ++++ Bacteroides_caccae 1 Clostridium_symbiosum +++ Bacteroides_sp_D20 1 Clostridium_symbiosum Clostridium_nexile 1 Clostridium_symbiosum + Coprococcus_catus 1 Clostridium_symbiosum − Coprococcus_comes 1 Clostridium_symbiosum Coprococcus_comes 1 Clostridium_symbiosum ++++ Dorea_formicigenerans 1 Clostridium_symbiosum Dorea_longicatena 1 Clostridium_symbiosum ++++ Faecalibacterium_prausnitzii 1 Clostridium_symbiosum Odoribacter_splanchnicus 1 Clostridium_symbiosum Parabacteroides_merdae 1 Clostridium_symbiosum − Roseburia_intestinalis 1 Clostridium_symbiosum −− Ruminococcus_obeum 1 Clostridium_symbiosum ++++ Ruminococcus_torques 1 Clostridium_symbiosum ++ Bacteroides_sp_D20 1 Collinsella_aerofaciens ++++ Clostridium_nexile 1 Collinsella_aerofaciens + Coprococcus_catus 1 Collinsella_aerofaciens ++++ Dorea_formicigenerans 1 Collinsella_aerofaciens ++ Dorea_longicatena 1 Collinsella_aerofaciens ++++ Faecalibacterium_prausnitzii 1 Collinsella_aerofaciens +++ Odoribacter_splanchnicus 1 Collinsella_aerofaciens +++ Parabacteroides_merdae 1 Collinsella_aerofaciens ++++ Roseburia_intestinalis 1 Collinsella_aerofaciens ++ Bacteroides_sp_D20 1 Escherichia_coli ++++ Clostridium_nexile 1 Escherichia_coli ++++ Coprococcus_catus 1 Escherichia_coli ++++ Dorea_formicigenerans 1 Escherichia_coli ++++ Dorea_longicatena 1 Escherichia_coli ++++ Faecalibacterium_prausnitzii 1 Escherichia_coli +++ Odoribacter_splanchnicus 1 Escherichia_coli +++ Parabacteroides_merdae 1 Escherichia_coli ++++ Roseburia_intestinalis 1 Escherichia_coli +++ Dorea_formicigenerans 1 Eubacterium_eligens −− Coprococcus_comes 1 Ruminococcus_gnavus ++++ Faecalibacterium_prausnitzii 1 Ruminococcus_gnavus ++++ Ruminococcus_bromii 1 Ruminococcus_gnavus ++++

Keystone OTUs Inhibit C. difficile Growth in a Competitive In Vitro Simulation Assay

TABLE 21 Net ID F-Score KEGG Orthology Pathways N968.S 16 KO:K00101, KO:K00116, KO:K00156, KO:K00163, KO:K00627, KO:K00656, KO:K00932, KO:K01069, KO:K01659, KO:K01720, KO:K01734, KO:K01908, KO:K03417, KO:K03777, KO:K03778, KO:K04020 N282.S 12 KO:K00004, KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03366, KO:K03778 N390.S 11 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K04020 N515.S 11 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K04020 N516.S 11 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K04020 N586 11 KO:K00102, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K01905, KO:K03778 N590.S 11 KO:K00004, KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03366, KO:K03778 N666.S 11 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K04020 N271.S 10 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03366, KO:K03778 N338.S 10 KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N368.S 10 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03366, KO:K03778 N381.S 10 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K10783 N382.S 10 KO:K00102, KO:K00627, KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K01905, KO:K03417, KO:K07246 N519.S 10 KO:K00004, KO:K00158, KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03366, KO:K03778 N535.S 10 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01067, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N597.S 10 KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N680.S 10 KO:K00102, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K01905, KO:K03778 N822.S 10 KO:K00004, KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03366, KO:K03778 N1008 9 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01659, KO:K01734, KO:K03778, KO:K04020 N329.S 9 KO:K00102, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N332.S 9 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N346.S 9 KO:K00116, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N353.S 9 KO:K00634, KO:K00656, KO:K00929, KO:K01067, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N361.S 9 KO:K00116, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N375.S 9 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N377.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N380.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N387.S 9 KO:K00102, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N396.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N397.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N415.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N419.S 9 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03366, KO:K03778 N431.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N434.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N440.S 9 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03417, KO:K03778, KO:K07246 N447.S 9 KO:K00634, KO:K00656, KO:K00929, KO:K01067, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N458.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N459.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N481.S 9 KO:K00102, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N526 9 KO:K00004, KO:K00116, KO:K00163, KO:K00627, KO:K00634, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N530.S 9 KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N534.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N591.S 9 KO:K00004, KO:K00158, KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03366, KO:K03778 N682.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N816.S 9 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N891.S 9 KO:K00102, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K01905, KO:K03778 N1091 8 KO:K00156, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734 N1093 8 KO:K00156, KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N262.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N279.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N284.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N288.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N290.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N301.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N302.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N310.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N312.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N323.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N325.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N331.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N336.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N339.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N340.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N341.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N343.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N344.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N345.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N352.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N355.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N356.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N357.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N358.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N369.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N370.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N372.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N373.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N374.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N376.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N386.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N389.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N394.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N400.S 8 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03417, KO:K07246 N405.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N408.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N422.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N423.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N429.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N430.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N432.S 8 KO:K00627, KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N437.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N450.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N477.S 8 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N478.S 8 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N482.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N490.S 8 KO:K00158, KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N493.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N509.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N543.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N547.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N582.S 8 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03417, KO:K03778, KO:K07246 N584.S 8 KO:K00102, KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03417, KO:K07246 N651.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N655.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N656.S 8 KO:K00156, KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N657.S 8 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N664 8 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778, KO:K10783 N667.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N675.S 8 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N693 8 KO:K00004, KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K01442, KO:K01734, KO:K03366 N698.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N712.S 8 KO:K00102, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N714.S 8 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N734.S 8 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01734, KO:K03778, KO:K04020 N782.S 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N789.S 8 KO:K00156, KO:K00163, KO:K00627, KO:K00656, KO:K01067, KO:K01069, KO:K01442, KO:K01734 N792 8 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778, KO:K10783 N794 8 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N817.S 8 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N844 8 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K04020 N851.S 8 KO:K00102, KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01734, KO:K04020 N876 8 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N1051 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01659, KO:K01734, KO:K03778 N402.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N403.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N414.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N416.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N433.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N448.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N451.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N460.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N462.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N466.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N470.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N479.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N480.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N484.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N511.S 7 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N518.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N520.S 7 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N524.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N542.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N580.S 7 KO:K00158, KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N587.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778, KO:K10783 N611.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N612.S 7 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03366, KO:K03778 N625.S 7 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03366 N649.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N685.S 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N686.S 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N687 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N733.S 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N739.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N777.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N785 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N788 7 KO:K00116, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01734, KO:K10783 N793.S 7 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734 N795.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778, KO:K10783 N798.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N804 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N807 7 KO:K00043, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N815.S 7 KO:K00102, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N829 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N836.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N846 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N875 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N894 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N898.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N913.S 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01734, KO:K03417, KO:K07246 N935 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N936.S 7 KO:K00156, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N945.S 7 KO:K00102, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N961 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N972 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N988 7 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N995.S 7 KO:K00627, KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N1002.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N1019.S 6 KO:K00156, KO:K00656, KO:K01067, KO:K01069, KO:K01659, KO:K01734 N1023 6 KO:K00627, KO:K00656, KO:K01442, KO:K01734, KO:K03366, KO:K03778 N1070.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01069, KO:K01442, KO:K01734 N399.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N421.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N436.S 6 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N439.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N441.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N446.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N457.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N464.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N465.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N468.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N469.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N474.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N488.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N508.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N510.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N512.S 6 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N514.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N517.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N521.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N522.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03417, KO:K07246 N523.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N525.S 6 KO:K00043, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N528.S 6 KO:K00656, KO:K01069, KO:K01734, KO:K03417, KO:K03778, KO:K07246 N537.S 6 KO:K00102, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N539.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N546.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N548.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N572.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N577.S 6 KO:K00627, KO:K00634, KO:K00656, KO:K01442, KO:K01734, KO:K03778 N581.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N602.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N614.S 6 KO:K00627, KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N617.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N621.S 6 KO:K00043, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N652.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N654.S 6 KO:K00116, KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N668.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N678.S 6 KO:K00156, KO:K00627, KO:K00656, KO:K01069, KO:K01659, KO:K01734 N681.S 6 KO:K00634, KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N710.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N741.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N769 6 KO:K00102, KO:K00656, KO:K01069, KO:K01659, KO:K01734, KO:K03778 N779 6 KO:K00158, KO:K00627, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N796.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N826.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N827.S 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N828 6 KO:K00158, KO:K00627, KO:K00634, KO:K00656, KO:K01442, KO:K01734 N832.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N840.S 6 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03366 N843.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N845 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N849 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N858 6 KO:K00043, KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N878 6 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N928.S 6 KO:K00634, KO:K00929, KO:K01067, KO:K01442, KO:K01734, KO:K03778 N960.S 6 KO:K00634, KO:K00656, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N1061 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N463.S 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N529.S 5 KO:K00656, KO:K01069, KO:K01659, KO:K01734, KO:K03778 N533.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N545 5 KO:K00634, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N570.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N574.S 5 KO:K00627, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N578.S 5 KO:K00656, KO:K01069, KO:K01659, KO:K01734, KO:K03778 N579.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N585.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N589.S 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N609.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N610.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N616.S 5 KO:K00634, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N623.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01659, KO:K01734 N648.S 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N653.S 5 KO:K00043, KO:K00656, KO:K01069, KO:K01442, KO:K01734 N665.S 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N672.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N689 5 KO:K00634, KO:K00656, KO:K01442, KO:K01734, KO:K10783 N730 5 KO:K00634, KO:K00656, KO:K01442, KO:K01734, KO:K03778 N737.S 5 KO:K00656, KO:K01069, KO:K01442, KO:K01734, KO:K03778 N797.S 5 KO:K00627, KO:K00656, KO:K01659, KO:K01734, KO:K03366 N800.S 5 KO:K00627, KO:K00656, KO:K01069, KO:K01442, KO:K01734 N802 5 KO:K00043, KO:K00627, KO:K00656, KO:K01442, KO:K01734 N830.S 5 KO:K00627, KO:K00634, KO:K00656, KO:K01442, KO:K01734 N833.S 5 KO:K00102, KO:K00634, KO:K00656, KO:K01442, KO:K01734 N835.S 5 KO:K00634, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N841 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N842.S 5 KO:K00634, KO:K00929, KO:K01442, KO:K01734, KO:K03778 N852 5 KO:K00656, KO:K01442, KO:K01659, KO:K01734, KO:K03778 N859 5 KO:K00102, KO:K00656, KO:K01069, KO:K01734, KO:K03778 N860 5 KO:K00627, KO:K00656, KO:K01069, KO:K01734, KO:K03778 N880 5 KO:K00634, KO:K00656, KO:K01069, KO:K01442, KO:K01734 N885 5 KO:K00043, KO:K00656, KO:K01442, KO:K01659, KO:K01734 N925 5 KO:K00158, KO:K00627, KO:K00656, KO:K01442, KO:K01734 N983 5 KO:K00627, KO:K00656, KO:K01442, KO:K01734, KO:K03366 N1004.S 4 KO:K00656, KO:K01069, KO:K01734, KO:K03778 N1078.S 4 KO:K00158, KO:K00627, KO:K00656, KO:K01069 N1088 4 KO:K00656, KO:K01069, KO:K01442, KO:K01734 N538.S 4 KO:K00656, KO:K01069, KO:K01734, KO:K03778 N604.S 4 KO:K00656, KO:K01659, KO:K01734, KO:K03778 N669.S 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N676.S 4 KO:K00656, KO:K01069, KO:K01734, KO:K03778 N690.S 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N692.S 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N695.S 4 KO:K00116, KO:K00656, KO:K01442, KO:K01734 N709 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N738.S 4 KO:K00656, KO:K01659, KO:K01734, KO:K03778 N775.S 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N776.S 4 KO:K00116, KO:K00656, KO:K01442, KO:K01734 N780.S 4 KO:K00656, KO:K01442, KO:K01659, KO:K01734 N781 4 KO:K00656, KO:K01069, KO:K01442, KO:K01734 N808.S 4 KO:K00656, KO:K01069, KO:K01734, KO:K10783 N809.S 4 KO:K00656, KO:K01069, KO:K01659, KO:K01734 N811.S 4 KO:K00116, KO:K00656, KO:K01069, KO:K01734 N869.S 4 KO:K00627, KO:K00656, KO:K01442, KO:K01734 N871.S 4 KO:K00656, KO:K01442, KO:K01659, KO:K01734 N881 4 KO:K00656, KO:K01442, KO:K01659, KO:K01734 N907.S 4 KO:K00656, KO:K01442, KO:K01659, KO:K01734 N927 4 KO:K00656, KO:K01067, KO:K01442, KO:K01734 N942 4 KO:K00102, KO:K00656, KO:K01442, KO:K01734 N947 4 KO:K00627, KO:K00656, KO:K01442, KO:K01734 N982 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N986.S 4 KO:K00656, KO:K01442, KO:K01734, KO:K03778 N987 4 KO:K00634, KO:K00656, KO:K01442, KO:K01734 N998.S 4 KO:K00656, KO:K01442, KO:K01659, KO:K01734 N1089 3 KO:K00656, KO:K01659, KO:K01734 N663.S 3 KO:K00656, KO:K01442, KO:K01734 N703.S 3 KO:K00656, KO:K01659, KO:K01734 N805.S 3 KO:K00656, KO:K01069, KO:K01442 N874.S 3 KO:K00656, KO:K01442, KO:K01734 N996 3 KO:K00656, KO:K01442, KO:K01734 N1092 2 KO:K01442, KO:K01734 N660.S 2 KO:K00656, KO:K01442

Functional Network Ecologies comprised of two or more OTUs that are observed in the ethanol-treated spore preparation or the combined engrafted and augmented ecologies of at least one patient post-treatment with the bacterial composition. Network Ecology IDs with a “.s” indicates that the network is a subset of the computationally determined networks reported in Table 8 with the same Network Ecology ID.

TABLE 22 Phylogenetic Clade OTUs in clade clade_172 Bifidobacteriaceae genomosp. C1, Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium animalis, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium gallicum, Bifidobacterium infantis, Bifidobacterium kashiwanohense, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum, Bifidobacterium scardovii, Bifidobacterium sp. HM2, Bifidobacterium sp. HMLN12, Bifidobacterium sp. M45, Bifidobacterium sp. MSX5B, Bifidobacterium sp. TM_7, Bifidobacterium thermophilum clade_172i Bifidobacteriaceae genomosp. C1, Bifidobacterium angulatum, Bifidobacterium animalis, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium gallicum, Bifidobacterium infantis, Bifidobacterium kashiwanohense, Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum, Bifidobacterium scardovii, Bifidobacterium sp. HM2, Bifidobacterium sp. HMLN12, Bifidobacterium sp. M45, Bifidobacterium sp. MSX5B, Bifidobacterium sp. TM_7, Bifidobacterium thermophilum clade_198 Lactobacillus casei, Lactobacillus paracasei, Lactobacillus zeae clade_198i Lactobacillus zeae clade_260 Clostridium hylemonae, Clostridium scindens, Lachnospiraceae bacterium 5_1_57FAA clade_260c Clostridium hylemonae, Lachnospiraceae bacterium 5_1_57FAA clade_260g Clostridium hylemonae, Lachnospiraceae bacterium 5_1_57FAA clade_260h Clostridium hylemonae, Lachnospiraceae bacterium 5_1_57FAA clade_262 Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris, Ruminococcus torques clade_262i Clostridium glycyrrhizinilyticum, Clostridium nexile, Coprococcus comes, Lachnospiraceae bacterium 1_1_57FAA, Lachnospiraceae bacterium 1_4_56FAA, Lachnospiraceae bacterium 8_1_57FAA, Ruminococcus lactaris clade_309 Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia producta, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus obeum, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_309c Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus obeum, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_309e Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus obeum, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_309g Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus obeum, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_309h Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus obeum, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_309i Blautia coccoides, Blautia glucerasea, Blautia glucerasei, Blautia hansenii, Blautia luti, Blautia schinkii, Blautia sp. M25, Blautia stercoris, Blautia wexlerae, Bryantella formatexigens, Clostridium coccoides, Eubacterium cellulosolvens, Lachnospiraceae bacterium 6_1_63FAA, Marvinbryantia formatexigens, Ruminococcus hansenii, Ruminococcus sp. 5_1_39BFAA, Ruminococcus sp. K_1, Syntrophococcus sucromutans clade_313 Lactobacillus antri, Lactobacillus coleohominis, Lactobacillus fermentum, Lactobacillus gastricus, Lactobacillus mucosae, Lactobacillus oris, Lactobacillus pontis, Lactobacillus reuteri, Lactobacillus sp. KLDS 1.0707, Lactobacillus sp. KLDS 1.0709, Lactobacillus sp. KLDS 1.0711, Lactobacillus sp. KLDS 1.0713, Lactobacillus sp. KLDS 1.0716, Lactobacillus sp. KLDS 1.0718, Lactobacillus sp. oral taxon 052, Lactobacillus vaginalis clade_313f Lactobacillus antri, Lactobacillus coleohominis, Lactobacillus fermentum, Lactobacillus gastricus, Lactobacillus mucosae, Lactobacillus oris, Lactobacillus pontis, Lactobacillus sp. KLDS 1.0707, Lactobacillus sp. KLDS 1.0709, Lactobacillus sp. KLDS 1.0711, Lactobacillus sp. KLDS 1.0713, Lactobacillus sp. KLDS 1.0716, Lactobacillus sp. KLDS 1.0718, Lactobacillus sp. oral taxon 052, Lactobacillus vaginalis clade_325 Staphylococcus aureus, Staphylococcus auricularis, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus carnosus, Staphylococcus cohnii, Staphylococcus condimenti, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus pasteuri, Staphylococcus pseudintermedius, Staphylococcus saccharolyticus, Staphylococcus saprophyticus, Staphylococcus sp. H292, Staphylococcus sp. H780, Staphylococcus sp. clone bottae7, Staphylococcus succinus, Staphylococcus warneri, Staphylococcus xylosus clade_325f Staphylococcus aureus, Staphylococcus auricularis, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus carnosus, Staphylococcus cohnii, Staphylococcus condimenti, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus pseudintermedius, Staphylococcus saccharolyticus, Staphylococcus saprophyticus, Staphylococcus sp. H292, Staphylococcus sp. H780, Staphylococcus sp. clone bottae7, Staphylococcus succinus, Staphylococcus xylosus clade_335 Bacteroides sp. 20_3, Bacteroides sp. 3_1_19, Bacteroides sp. 3_2_5, Parabacteroides distasonis, Parabacteroides goldsteinii, Parabacteroides gordonii, Parabacteroides sp. D13 clade_335i Bacteroides sp. 20_3, Bacteroides sp. 3119, Bacteroides sp. 3_2_5, Parabacteroides goldsteinii, Parabacteroides gordonii, Parabacteroides sp. D13 clade_351 Clostridium innocuum, Clostridium sp. HGF2 clade_351e Clostridium sp. HGF2 clade_354 Clostridium bartlettii, Clostridium bifermentans, Clostridium ghonii, Clostridium glycolicum, Clostridium mayombei, Clostridium sordellii, Clostridium sp. MT4 E, Eubacterium tenue clade_354e Clostridium bartlettii, Clostridium ghonii, Clostridium glycolicum, Clostridium mayombei, Clostridium sordellii, Clostridium sp. MT4 E, Eubacterium tenue clade_360 Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, Ruminococcus sp. ID8 clade_360c Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus clade_360g Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus clade_360h Dorea formicigenerans, Dorea longicatena, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus clade_360i Dorea formicigenerans, Lachnospiraceae bacterium 2_1_46FAA, Lachnospiraceae bacterium 2_1_58FAA, Lachnospiraceae bacterium 4_1_37FAA, Lachnospiraceae bacterium 9_1_43BFAA, Ruminococcus gnavus, Ruminococcus sp. ID8 clade_378 Bacteroides barnesiae, Bacteroides coprocola, Bacteroides coprophilus, Bacteroides dorei, Bacteroides massiliensis, Bacteroides plebeius, Bacteroides sp. 3_1_33FAA, Bacteroides sp. 3_1_40A, Bacteroides sp. 4_3_47FAA, Bacteroides sp. 9_1_42FAA, Bacteroides sp. NB_8, Bacteroides vulgatus clade_378e Bacteroides barnesiae, Bacteroides coprocola, Bacteroides coprophilus, Bacteroides dorei, Bacteroides massiliensis, Bacteroides plebeius, Bacteroides sp. 3_1_33FAA, Bacteroides sp. 3_1_40A, Bacteroides sp. 4_3_47FAA, Bacteroides sp. 9_1_42FAA, Bacteroides sp. NB_8 clade_38 Bacteroides ovatus, Bacteroides sp. 1_1_30, Bacteroides sp. 2_1_22, Bacteroides sp. 2_2_4, Bacteroides sp. 3_1_23, Bacteroides sp. D1, Bacteroides sp. D2, Bacteroides sp. D22, Bacteroides xylanisolvens clade_38e Bacteroides sp. 1_1_30, Bacteroides sp. 2_1_22, Bacteroides sp. 2_2_4, Bacteroides sp. 3_1_23, Bacteroides sp. D1, Bacteroides sp. D2, Bacteroides sp. D22, Bacteroides xylanisolvens clade_38i Bacteroides sp. 1_1_30, Bacteroides sp. 2_1_22, Bacteroides sp. 2_2_4, Bacteroides sp. 3_1_23, Bacteroides sp. D1, Bacteroides sp. D2, Bacteroides sp. D22, Bacteroides xylanisolvens clade_408 Anaerostipes caccae, Anaerostipes sp. 3_2_56FAA, Clostridiales bacterium 1_7_47FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium asparagiforme, Clostridium bolteae, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium hathewayi, Clostridium indolis, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 3_1_57FAA, Lachnospiraceae bacterium 5_1_63FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_408b Anaerostipes caccae, Anaerostipes sp. 3_2_56FAA, Clostridiales bacterium 1_7_47FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium asparagiforme, Clostridium bolteae, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium indolis, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 5_1_63FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_408d Anaerostipes caccae, Anaerostipes sp. 3_2_56FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium hathewayi, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 3_1_57FAA, Lachnospiraceae bacterium 5_1_63FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_408f Anaerostipes sp. 3_2_56FAA, Clostridiales bacterium 1_7_47FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium asparagiforme, Clostridium bolteae, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium hathewavi, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 3_1_57FAA, Lachnospiraceae bacterium 5163FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_408g Anaerostipes caccae, Anaerostipes sp. 3_2_56FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 5_1_63FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_408h Anaerostipes caccae, Anaerostipes sp. 3_2_56FAA, Clostridiales sp. SM4_1, Clostridiales sp. SSC_2, Clostridium aerotolerans, Clostridium aldenense, Clostridium algidixylanolyticum, Clostridium amygdalinum, Clostridium celerecrescens, Clostridium citroniae, Clostridium clostridiiformes, Clostridium clostridioforme, Clostridium lavalense, Clostridium saccharolyticum, Clostridium sp. M62_1, Clostridium sp. SS2_1, Clostridium sphenoides, Clostridium symbiosum, Clostridium xylanolyticum, Eubacterium hadrum, Fusobacterium naviforme, Lachnospiraceae bacterium 5_1_63FAA, Lachnospiraceae bacterium A4, Lachnospiraceae bacterium DJF VP30, Lachnospiraceae genomosp. C1, Moryella indoligenes clade_420 Barnesiella intestinihominis, Barnesiella viscericola, Parabacteroides sp. NS31_3, Porphyromonadaceae bacterium NML 060648, Tannerella forsythia, Tannerella sp. 6_1_58FAA_CT1 clade_420f Barnesiella viscericola, Parabacteroides sp. NS31_3, Porphyromonadaceae bacterium NML 060648, Tannerella forsythia, Tannerella sp. 6_1_58FAA_CT1 clade_444 Butyrivibrio fibrisolvens, Eubacterium rectale, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecalis, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, Shuttleworthia sp. oral taxon G69 clade_444i Butyrivibrio fibrisolvens, Eubacterium sp. oral clone GI038, Lachnobacterium bovis, Roseburia cecicola, Roseburia faecis, Roseburia hominis, Roseburia inulinivorans, Roseburia sp. 11SE37, Roseburia sp. 11SE38, Shuttleworthia satelles, Shuttleworthia sp. MSX8B, Shuttleworthia sp. oral taxon G69 clade_478 Faecalibacterium prausnitzii, Gemmiger formicilis, Subdoligranulum variabile clade_478i Gemmiger formicilis, Subdoligranulum variabile clade_479 Clostridiaceae bacterium JC13, Clostridium sp. MLG055, Erysipelotrichaceae bacterium 3_1_53 clade_479c Clostridium sp. MLG055, Erysipelotrichaceae bacterium 3_1_53 clade_479g Clostridium sp. MLG055, Erysipelotrichaceae bacterium 3_1_53 clade_479h Clostridium sp. MLG055, Erysipelotrichaceae bacterium 3_1_53 clade_481 Clostridium cocleatum, Clostridium ramosum, Clostridium saccharogumia, Clostridium spiroforme, Coprobacillus sp. D7 clade_481a Clostridium cocleatum, Clostridium spiroforme, Coprobacillus sp. D7 clade_481b Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme, Coprobacillus sp. D7 clade_481e Clostridium cocleatum, Clostridium saccharogumia, Clostridium spiroforme, Coprobacillus sp. D7 clade_481g Clostridium cocleatum, Clostridium spiroforme, Coprobacillus sp. D7 clade_481h Clostridium cocleatum, Clostridium spiroforme, Coprobacillus sp. D7 clade_481i Clostridium ramosum, Clostridium saccharogumia, Clostridium spiroforme, Coprobacillus sp. D7 clade_497 Abiotrophia para _(—) adiacens, Carnobacterium divergens, Carnobacterium maltaromaticum, Enterococcus avium, Enterococcus caccae, Enterococcus casseliflavus, Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus gilvus, Enterococcus hawaiiensis, Enterococcus hirae, Enterococcus italicus, Enterococcus mundtii, Enterococcus raffinosus, Enterococcus sp. BV2CASA2, Enterococcus sp. CCRI 16620, Enterococcus sp. F95, Enterococcus sp. RfL6, Enterococcus thailandicus, Fusobacterium canifelinum, Fusobacterium genomosp. C1, Fusobacterium genomosp. C2, Fusobacterium nucleatum, Fusobacterium periodonticum, Fusobacterium sp. 11_3_2, Fusobacterium sp. 1_1_41FAA, Fusobacterium sp. 2_1_31, Fusobacterium sp. 3_1_27, Fusobacterium sp. 3_1_33, Fusobacterium sp. 3_1_36A2, Fusobacterium sp. AC18, Fusobacterium sp. ACB2, Fusobacterium sp. AS2, Fusobacterium sp. CM1, Fusobacterium sp. CM21, Fusobacterium sp. CM22, Fusobacterium sp. oral clone ASCF06, Fusobacterium sp. oral clone ASCF11, Granulicatella adiacens, Granulicatella elegans, Granulicatella paradiacens, Granulicatella sp. oral clone ASC02, Granulicatella sp. oral clone ASCA05, Granulicatella sp. oral clone ASCB09, Granulicatella sp. oral clone ASCG05, Tetragenococcus halophilus, Tetragenococcus koreensis, Vagococcus fluvialis clade_497e Abiotrophia para _(—) adiacens, Carnobacterium divergens, Carnobacterium maltaromaticum, Enterococcus avium, Enterococcus caccae, Enterococcus casseliflavus, Enterococcus durans, Enterococcus faecium, Enterococcus gallinarum, Enterococcus gilvus, Enterococcus hawaiiensis, Enterococcus hirae, Enterococcus italicus, Enterococcus mundtii, Enterococcus raffinosus, Enterococcus sp. BV2CASA2, Enterococcus sp. CCRI 16620, Enterococcus sp. F95, Enterococcus sp. RfL6, Enterococcus thailandicus, Fusobacterium canifelinum, Fusobacterium genomosp. C1, Fusobacterium genomosp. C2, Fusobacterium nucleatum, Fusobacterium periodonticum, Fusobacterium sp. 11_3_2, Fusobacterium sp. 1_1_41FAA, Fusobacterium sp. 2_1_31, Fusobacterium sp. 3_1_27, Fusobacterium sp. 3_1_33, Fusobacterium sp. 3_1_36A2, Fusobacterium sp. AC18, Fusobacterium sp. ACB2, Fusobacterium sp. AS2, Fusobacterium sp. CM1, Fusobacterium sp. CM21, Fusobacterium sp. CM22, Fusobacterium sp. oral clone ASCF06, Fusobacterium sp. oral clone ASCF11, Granulicatella adiacens, Granulicatella elegans, Granulicatella paradiacens, Granulicatella sp. oral clone ASC02, Granulicatella sp. oral clone ASCA05, Granulicatella sp. oral clone ASCB09, Granulicatella sp. oral clone ASCG05, Tetragenococcus halophilus, Tetragenococcus koreensis, Vagococcus fluvialis clade_497f Abiotrophia para _(—) adiacens, Carnobacterium divergens, Carnobacterium maltaromaticum, Enterococcus avium, Enterococcus caccae, Enterococcus casseliflavus, Enterococcus faecalis, Enterococcus gallinarum, Enterococcus gilvus, Enterococcus hawaiiensis, Enterococcus italicus, Enterococcus mundtii, Enterococcus raffinosus, Enterococcus sp. BV2CASA2, Enterococcus sp. CCRI 16620, Enterococcus sp. F95, Enterococcus sp. RfL6, Enterococcus thailandicus, Fusobacterium canifelinum, Fusobacterium genomosp. C1, Fusobacterium genomosp. C2, Fusobacterium nucleatum, Fusobacterium periodonticum, Fusobacterium sp. 11_3_2, Fusobacterium sp. 1_1_41FAA, Fusobacterium sp. 2_1_31, Fusobacterium sp. 3_1_27, Fusobacterium sp. 3_1_33, Fusobacterium sp. 3_1_36A2, Fusobacterium sp. AC18, Fusobacterium sp. ACB2, Fusobacterium sp. AS2, Fusobacterium sp. CM1, Fusobacterium sp. CM21, Fusobacterium sp. CM22, Fusobacterium sp. oral clone ASCF06, Fusobacterium sp. oral clone ASCF11, Granulicatella adiacens, Granulicatella elegans, Granulicatella paradiacens, Granulicatella sp. oral clone ASC02, Granulicatella sp. oral clone ASCA05, Granulicatella sp. oral clone ASCB09, Granulicatella sp. oral clone ASCG05, Tetragenococcus halophilus, Tetragenococcus koreensis, Vagococcus fluvialis clade_512 Eubacterium barkeri, Eubacterium callanderi, Eubacterium limosum, Pseudoramibacter alactolyticus clade_512i Eubacterium barkeri, Eubacterium callanderi, Pseudoramibacter alactolyticus clade_516 Anaerotruncus colihominis, Clostridium methylpentosum, Clostridium sp. YIT 12070, Hydrogenoanaerobacterium saccharovorans, Ruminococcus albus, Ruminococcus flavefaciens clade 516c Clostridium methylpentosum, Clostridium sp. YIT 12070, Hydrogenoanaerobacterium saccharovorans, Ruminococcus albus, Ruminococcus flavefaciens clade_516g Clostridium methylpentosum, Clostridium sp. YIT 12070, Hydrogenoanaerobacterium saccharovorans, Ruminococcus albus, Ruminococcus flavefaciens clade_516h Clostridium methylpentosum, Clostridium sp. YIT 12070, Hydrogenoanaerobacterium saccharovorans, Ruminococcus albus, Ruminococcus flavefaciens clade_519 Eubacterium ventriosum clade_522 Bacteroides galacturonicus, Eubacterium eligens, Lachnospira multipara, Lachnospira pectinoschiza, Lactobacillus rogosae clade_522i Bacteroides galacturonicus, Lachnospira multipara, Lachnospira pectinoschiza, Lactobacillus rogosae clade_553 Collinsella aerofaciens, Collinsella intestinalis, Collinsella stercoris, Collinsella tanakaei clade_553i Collinsella intestinalis, Collinsella stercoris, Collinsella tanakaei clade_566 Adlercreutzia equolifaciens, Coriobacteriaceae bacterium JC110, Coriobacteriaceae bacterium phI, Cryptobacterium curtum, Eggerthella lenta, Eggerthella sinensis, Eggerthella sp. 1_3_56FAA, Eggerthella sp. HGA1, Eggerthella sp. YY7918, Gordonibacter pamelaeae, Slackia equolifaciens, Slackia exigua, Slackia faecicanis, Slackia heliotrinireducens, Slackia isoflavoniconvertens, Slackia piriformis, Slackia sp. NATTS, Streptomyces albus clade_566f Coriobacteriaceae bacterium JC110, Coriobacteriaceae bacterium phI, Cryptobacterium curtum, Eggerthella lenta, Eggerthella sinensis, Eggerthella sp. 1_3_56FAA, Eggerthella sp. HGA1, Eggerthella sp. YY7918, Gordonibacter pamelaeae, Slackia equolifaciens, Slackia exigua, Slackia faecicanis, Slackia heliotrinireducens, Slackia isoflavoniconvertens, Slackia piriformis, Slackia sp. NATTS, Streptomyces albus clade_572 Butyricicoccus pullicaecorum, Eubacterium desmolans, Papillibacter cinnamivorans, Sporobacter termitidis clade_572i Butyricicoccus pullicaecorum, Papillibacter cinnamivorans, Sporobacter termitidis clade_65 Bacteroides faecis, Bacteroides fragilis, Bacteroides nordii, Bacteroides salyersiae, Bacteroides sp. 1_1_14, Bacteroides sp. 1_1_6, Bacteroides sp. 2_1_56FAA, Bacteroides sp. AR29, Bacteroides sp. B2, Bacteroides thetaiotaomicron clade_65e Bacteroides faecis, Bacteroides fragilis, Bacteroides nordii, Bacteroides salyersiae, Bacteroides sp. 1_1_14, Bacteroides sp. 1_1_6, Bacteroides sp. 2_1_56FAA, Bacteroides sp. AR29, Bacteroides sp. B2 clade_92 Actinobacillus actinomycetemcomitans, Actinobacillus succinogenes, Aggregatibacter actinomycetemcomitans, Aggregatibacter aphrophilus, Aggregatibacter segnis, Avetyella dalhousiensis, Bisgaard Taxon, Buchnera aphidicola, Cedecea davisae, Citrobacter amalonaticus, Citrobacter braakii, Citrobacter farmeri, Citrobacter freundii, Citrobacter gillenii, Citrobacter koseri, Citrobacter murliniae, Citrobacter rodentium, Citrobacter sedlakii, Citrobacter sp. 30_2, Citrobacter sp. KMSI_3, Citrobacter werkmanii, Citrobacter youngae, Cronobacter malonaticus, Cronobacter sakazakii, Cronobacter turicensis, Enterobacter aerogenes, Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter cowanii, Enterobacter hormaechei, Enterobacter sp. 247BMC, Enterobacter sp. 638, Enterobacter sp. JC163, Enterobacter sp. SCSS, Enterobacter sp. TSE38, Enterobacteriaceae bacterium 9_2_54FAA, Enterobacteriaceae bacterium CF01Ent_1, Enterobacteriaceae bacterium Smarlab 3302238, Escherichia albertii, Escherichia coli, Escherichia fergusonii, Escherichia hermannii, Escherichia sp. 1_1_43, Escherichia sp. 4_1_40B, Escherichia sp. B4, Escherichia vulneris, Ewingella americana, Haemophilus genomosp. P2 oral clone MB3_C24, Haemophilus genomosp. P3 oral clone MB3_C38, Haemophilus sp. oral clone JM053, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella sp. AS10, Klebsiella sp. Co9935, Klebsiella sp. OBRC7, Klebsiella sp. SP_BA, Klebsiella sp. SRC_DSD1, Klebsiella sp. SRC_DSD11, Klebsiella sp. SRC_DSD12, Klebsiella sp. SRC_DSD15, Klebsiella sp. SRC_DSD2, Klebsiella sp. SRC_DSD6, Klebsiella sp. enrichment culture clone SRC_DSD25, Klebsiella variicola, Kluyvera ascorbata, Kluyvera cryocrescens, Leminorella grimontii, Leminorella richardii, Pantoea agglomerans, Pantoea ananatis, Pantoea brenneri, Pantoea citrea, Pantoea conspicua, Pantoea septica, Pasteurella dagmatis, Pasteurella multocida, Plesiomonas shigelloides, Raoultella ornithinolytica, Raoultella planticola, Raoultella terrigena, Salmonella bongori, Salmonella enterica, Salmonella typhimurium, Serratia fonticola, Serratia liquefaciens, Serratia marcescens, Serratia odorifera, Serratia proteamaculans, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Tatumella ptyseos, Trabulsiella guamensis, Yersinia aldovae, Yersinia aleksiciae, Yersinia bercovieri, Yersinia enterocolitica, Yersinia frederiksenii, Yersinia intermedia, Yersinia kristensenii, Yersinia mollaretii, Yersinia pestis, Yersinia pseudotuberculosis, Yersinia rohdei, Yokenella regensburgei clade_92e Actinobacillus actinomycetemcomitans, Actinobacillus succinogenes, Aggregatibacter actinomycetemcomitans, Aggregatibacter aphrophilus, Aggregatibacter segnis, Averyella dalhousiensis, Bisgaard Taxon, Buchnera aphidicola, Cedecea davisae, Citrobacter amalonaticus, Citrobacter braakii, Citrobacter farmeri, Citrobacter freundii, Citrobacter gillenii, Citrobacter koseri, Citrobacter murliniae, Citrobacter rodentium, Citrobacter sedlakii, Citrobacter sp. 30_2, Citrobacter sp. KMSI_3, Citrobacter werkmanii, Citrobacter youngae, Cronobacter malonaticus, Cronobacter sakazakii, Cronobacter turicensis, Enterobacter aerogenes, Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter cowanii, Enterobacter hormaechei, Enterobacter sp. 247BMC, Enterobacter sp. 638, Enterobacter sp. JC163, Enterobacter sp. SCSS, Enterobacter sp. TSE38, Enterobacteriaceae bacterium 9_2_54FAA, Enterobacteriaceae bacterium CF01Ent_1, Enterobacteriaceae bacterium Smarlab 3302238, Escherichia albertii, Escherichia fergusonii, Escherichia hermannii, Escherichia sp. 1_1_43, Escherichia sp. 4_1_40B, Escherichia sp. B4, Escherichia vulneris, Ewingella americana, Haemophilus genomosp. P2 oral clone MB3_C24, Haemophilus genomosp. P3 oral clone MB3_C38, Haemophilus sp. oral clone JM053, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella sp. AS10, Klebsiella sp. Co9935, Klebsiella sp. OBRC7, Klebsiella sp. SP_BA, Klebsiella sp. SRC_DSD1, Klebsiella sp. SRC_DSD11, Klebsiella sp. SRC_DSD12, Klebsiella sp. SRC_DSD15, Klebsiella sp. SRC_DSD2, Klebsiella sp. SRC_DSD6, Klebsiella sp. enrichment culture clone SRC_DSD25, Klebsiella variicola, Kluyvera ascorbata, Kluyvera cryocrescens, Leminorella grimontii, Leminorella richardii, Pantoea agglomerans, Pantoea ananatis, Pantoea brenneri, Pantoea citrea, Pantoea conspicua, Pantoea septica, Pasteurella dagmatis, Pasteurella multocida, Plesiomonas shigelloides, Raoultella ornithinolytica, Raoultella planticola, Raoultella terrigena, Salmonella bongori, Salmonella enterica, Salmonella typhimurium, Serratia fonticola, Serratia liquefaciens, Serratia marcescens, Serratia odorifera, Serratia proteamaculans, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Tatumella ptyseos, Trabulsiella guamensis, Yersinia aldovae, Yersinia aleksiciae, Yersinia bercovieri, Yersinia enterocolitica, Yersinia frederiksenii, Yersinia intermedia, Yersinia kristensenii, Yersinia mollaretii, Yersinia pestis, Yersinia pseudotuberculosis, Yersinia rahdei, Yokenella regensburgei clade_92i Actinobacillus actinomycetemcomitans, Actinobacillus succinogenes, Aggregatibacter actinomycetemcomitans, Aggregatibacter aphrophilus, Aggregatibacter segnis, Averyella dalhousiensis, Bisgaard Taxon, Buchnera aphidicola, Cedecea davisae, Citrobacter amalonaticus, Citrobacter braakii, Citrobacter farmeri, Citrobacter freundii, Citrobacter gillenii, Citrobacter koseri, Citrobacter murliniae, Citrobacter rodentium, Citrobacter sedlakii, Citrobacter sp. 30_2, Citrobacter sp. KMSI_3, Citrobacter werkmanii, Citrobacter youngae, Cronobacter malonaticus, Cronobacter sakazakii, Cronobacter turicensis, Enterobacter aerogenes, Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter cowanii, Enterobacter hormaechei, Enterobacter sp. 247BMC, Enterobacter sp. 638, Enterobacter sp. JC163, Enterobacter sp. SCSS, Enterobacter sp. TSE38, Enterobacteriaceae bacterium 9_2_54FAA, Enterobacteriaceae bacterium CF01Ent_1, Enterobacteriaceae bacterium Smarlab 3302238, Escherichia albertii, Escherichia fergusonii, Escherichia hermannii, Escherichia sp. 1_1_43, Escherichia sp. 4_1_40B, Escherichia sp. B4, Escherichia vulneris, Ewingella americana, Haemophilus genomosp. P2 oral clone MB3_C24, Haemophilus genomosp. P3 oral clone MB3_C38, Haemophilus sp. oral clone JM053, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella sp. AS10, Klebsiella sp. Co9935, Klebsiella sp. OBRC7, Klebsiella sp. SP_BA, Klebsiella sp. SRC_DSD1, Klebsiella sp. SRC_DSD11, Klebsiella sp. SRC_DSD12, Klebsiella sp. SRC_DSD15, Klebsiella sp. SRC_DSD2, Klebsiella sp. SRC_DSD6, Klebsiella sp. enrichment culture clone SRC_DSD25, Klebsiella variicola, Kluyvera ascorbata, Kluyvera cryocrescens, Leminorella grimontii, Leminorella richardii, Pantoea agglomerans, Pantoea ananatis, Pantoea brenneri, Pantoea citrea, Pantoea conspicua, Pantoea septica, Pasteurella dagmatis, Pasteurella multocida, Plesiomonas shigelloides, Raoultella ornithinolytica, Raoultella planticola, Raoultella terrigena, Salmonella bongori, Salmonella enterica, Salmonella typhimurium, Serratia fonticola, Serratia liquefaciens, Serratia marcescens, Serratia odorifera, Serratia proteamaculans, Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Tatumella ptyseos, Trabulsiella guamensis, Yersinia aldovae, Yersinia aleksiciae, Yersinia bercovieri, Yersinia enterocolitica, Yersinia frederiksenii, Yersinia intermedia, Yersinia kristensenii, Yersinia mollaretii, Yersinia pestis, Yersinia pseudotuberculosis, Yersinia rohdei, Yokenella regensburgei clade_96 Clostridium oroticum, Clostridium sp. D5, Eubacterium contortum, Eubacterium fissicatena clade_96g Clostridium oroticum, Clostridium sp. D5, Eubacterium fissicatena clade_96h Clostridium oroticum, Clostridium sp. D5, Eubacterium fissicatena clade_98 Okadaella gastrococcus, Streptococcus agalactiae, Streptococcus alactolyticus, Streptococcus australis, Streptococcus bovis, Streptococcus canis, Streptococcus constellatus, Streptococcus cristatus, Streptococcus dysgalactiae, Streptococcus equi, Streptococcus equinus, Streptococcus gallolyticus, Streptococcus genomosp. C1, Streptococcus genomosp. C2, Streptococcus genomosp. C3, Streptococcus genomosp. C4, Streptococcus genomosp. C5, Streptococcus genomosp. C6, Streptococcus genomosp. C7, Streptococcus genomosp. C8, Streptococcus gordonii, Streptococcus infantarius, Streptococcus infantis, Streptococcus intermedius, Streptococcus lutetiensis, Streptococcus massiliensis, Streptococcus mitis, Streptococcus oligofermentans, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus pasteurianus, Streptococcus peroris, Streptococcus pneumoniae, Streptococcus porcinus, Streptococcus pseudopneumoniae, Streptococcus pseudoporcinus, Streptococcus pyogenes, Streptococcus ratti, Streptococcus salivarius, Streptococcus sanguinis, Streptococcus sinensis, Streptococcus sp. 2285_97, Streptococcus sp. 2_1_36FAA, Streptococcus sp. ACS2, Streptococcus sp. AS20, Streptococcus sp. BS35a, Streptococcus sp. C150, Streptococcus sp. CM6, Streptococcus sp. ICM10, Streptococcus sp. ICM12, Streptococcus sp. ICM2, Streptococcus sp. ICM4, Streptococcus sp. ICM45, Streptococcus sp. M143, Streptococcus sp. M334, Streptococcus sp. oral clone ASB02, Streptococcus sp. oral clone ASCA03, Streptococcus sp. oral clone ASCA04, Streptococcus sp. oral clone ASCA09, Streptococcus sp. oral clone ASCB04, Streptococcus sp. oral clone ASCB06, Streptococcus sp. oral clone ASCC04, Streptococcus sp. oral clone ASCC05, Streptococcus sp. oral clone ASCC12, Streptococcus sp. oral clone ASCD01, Streptococcus sp. oral clone ASCD09, Streptococcus sp. oral clone ASCD10, Streptococcus sp. oral clone ASCE03, Streptococcus sp. oral clone ASCE04, Streptococcus sp. oral clone ASCE05, Streptococcus sp. oral clone ASCE06, Streptococcus sp. oral clone ASCE09, Streptococcus sp. oral clone ASCE10, Streptococcus sp. oral clone ASCE12, Streptococcus sp. oral clone ASCF05, Streptococcus sp. oral clone ASCF07, Streptococcus sp. oral clone ASCF09, Streptococcus sp. oral clone ASCG04, Streptococcus sp. oral clone BW009, Streptococcus sp. oral clone CH016, Streptococcus sp. oral clone GK051, Streptococcus sp. oral clone GM006, Streptococcus sp. oral clone P2PA_41 P2, Streptococcus sp. oral clone P4PA_30 P4, Streptococcus sp. oral taxon 071, Streptococcus sp. oral taxon G59, Streptococcus sp. oral taxon G62, Streptococcus sp. oral taxon G63, Streptococcus suis, Streptococcus thermophilus, Streptococcus uberis, Streptococcus urinalis, Streptococcus vestibularis, Streptococcus viridans, Synergistetes bacterium oral clone 03 5 D05 clade_98i Okadaella gastrococcus, Streptococcus agalactiae, Streptococcus alactolyticus, Streptococcus australis, Streptococcus bovis, Streptococcus canis, Streptococcus constellatus, Streptococcus cristatus, Streptococcus dysgalactiae, Streptococcus equi, Streptococcus equinus, Streptococcus gallolyticus, Streptococcus genomosp. C1, Streptococcus genomosp. C2, Streptococcus genomosp. C3, Streptococcus genomosp. C4, Streptococcus genomosp. C5, Streptococcus genomosp. C6, Streptococcus genomosp. C7, Streptococcus genomosp. C8, Streptococcus gordonii, Streptococcus infantarius, Streptococcus infantis, Streptococcus intermedius, Streptococcus lutetiensis, Streptococcus massiliensis, Streptococcus oligofermentans, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus pasteurianus, Streptococcus peroris, Streptococcus pneumoniae, Streptococcus porcinus, Streptococcus pseudopneumoniae, Streptococcus pseudoporcinus, Streptococcus pyogenes, Streptococcus ratti, Streptococcus salivarius, Streptococcus sanguinis, Streptococcus sinensis, Streptococcus sp. 2285_97, Streptococcus sp. 2_1_36FAA, Streptococcus sp. ACS2, Streptococcus sp. AS20, Streptococcus sp. BS35a, Streptococcus sp. C150, Streptococcus sp. CM6, Streptococcus sp. ICM10, Streptococcus sp. ICM12, Streptococcus sp. ICM2, Streptococcus sp. ICM4, Streptococcus sp. ICM45, Streptococcus sp. M143, Streptococcus sp. M334, Streptococcus sp. oral clone ASB02, Streptococcus sp. oral clone ASCA03, Streptococcus sp. oral clone ASCA04, Streptococcus sp. oral clone ASCA09, Streptococcus sp. oral clone ASCB04, Streptococcus sp. oral clone ASCB06, Streptococcus sp. oral clone ASCC04, Streptococcus sp. oral clone ASCC05, Streptococcus sp. oral clone ASCC12, Streptococcus sp. oral clone ASCD01, Streptococcus sp. oral clone ASCD09, Streptococcus sp. oral clone ASCD10, Streptococcus sp. oral clone ASCE03, Streptococcus sp. oral clone ASCE04, Streptococcus sp. oral clone ASCE05, Streptococcus sp. oral clone ASCE06, Streptococcus sp. oral clone ASCE09, Streptococcus sp. oral clone ASCE10, Streptococcus sp. oral clone ASCE12, Streptococcus sp. oral clone ASCF05, Streptococcus sp. oral clone ASCF07, Streptococcus sp. oral clone ASCF09, Streptococcus sp. oral clone ASCG04, Streptococcus sp. oral clone BW009, Streptococcus sp. oral clone CH016, Streptococcus sp. oral clone GK051, Streptococcus sp. oral clone GM006, Streptococcus sp. oral clone P2PA_41 P2, Streptococcus sp. oral clone P4PA_30 P4, Streptococcus sp. oral taxon 071, Streptococcus sp. oral taxon G59, Streptococcus sp. oral taxon G62. Streptococcus sp. oral taxon G63, Streptococcus suis, Streptococcus thermophilus, Streptococcus uberis, Streptococcus urinalis, Streptococcus vestibularis, Streptococcus viridans, Synergistetes bacterium oral clone 03 5 DOS

Phylogenetic Clades with Alternative Embodiments

LENGTHY TABLES The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20180353554A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3). 

1.-128. (canceled)
 129. A method of treating, preventing, or reducing the severity of a disorder selected from the group consisting of Clostridium difficile infection and ulcerative colitis, comprising: administering to a mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, the therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, wherein the plurality of isolated bacteria or the purified bacterial preparation comprises: a first bacterial operational taxonomic units (OTU) comprising a 16S rDNA comprising a sequence at least 97% identical to SEQ ID NO: 674, a second bacterial OTU comprising a 16S rDNA comprising a sequence at least 97% identical to SEQ ID NO: 856, and a third bacterial OTU comprising a 16S rDNA comprising a sequence at least 97% identical SEQ ID NO:
 1639. 130. A method of treating, preventing, or reducing the severity of a disorder selected from the group consisting of Clostridium difficile infection and ulcerative colitis, comprising: administering to a mammalian subject in need thereof an effective amount of a therapeutic bacterial composition, the therapeutic bacterial composition comprising a plurality of isolated bacteria or a purified bacterial preparation, wherein the plurality of isolated bacteria or the purified bacterial preparation comprises a Coprococcus comes, an Eubacterium rectale, and a Roseburia inulinivorans.
 131. The method of claim 129, wherein the first bacterial OTU comprises a 16S rDNA comprising SEQ ID NO: 674, the second bacterial OTU comprises a 16S rDNA comprising SEQ ID NO: 856, and the third bacterial OTU comprises a 16S rDNA comprising SEQ ID NO:
 1639. 132. The method of claim 129, wherein the therapeutic bacterial composition is substantially depleted of a residual habitat product of a fecal material.
 133. The method of claim 129, wherein the therapeutic bacterial composition is capable of inducing the formation of IgA, RegIII-gamma, IL-10, regulatory T cells, TGF-beta, alpha-defensin, beta-defensin, or an antimicrobial peptide in the mammalian subject.
 134. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form including at least one pharmaceutically acceptable carrier.
 135. The method of claim 134, wherein the oral finished pharmaceutical dosage form comprises at least about 1×10⁴ colony forming units of the bacteria per dose of the composition.
 136. The method of claim 134, wherein the oral finished pharmaceutical dosage form is a capsule.
 137. The method of claim 134, wherein the oral finished pharmaceutical dosage form is a tablet.
 138. The method of claim 134, wherein the oral finished pharmaceutical dosage form is a powder.
 139. The method of claim 129, wherein the therapeutic bacterial composition is prepared by ethanol treatment.
 140. The method of claim 129, wherein the therapeutic bacterial composition is prepared by heat treatment.
 141. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form comprising at least 1×10⁴ colony forming units of the bacteria per dose of the composition and including at least one pharmaceutically acceptable carrier and the therapeutic bacterial composition is prepared by ethanol treatment.
 142. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form comprising at least 1×10⁴ colony forming units of the bacteria per dose of the composition and including at least one pharmaceutically acceptable carrier and the therapeutic bacterial composition is prepared by heat treatment.
 143. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form comprising at least 1×10⁴ colony forming units of the bacteria per dose of the composition and including at least one pharmaceutically acceptable carrier and the therapeutic bacterial composition is prepared by ethanol treatment, and wherein the therapeutic bacterial composition is substantially depleted of a residual habitat product of a fecal material.
 144. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form comprising at least 1×10⁴ colony forming units of the bacteria per dose of the composition and including at least one pharmaceutically acceptable carrier and the therapeutic bacterial composition is prepared by heat treatment, and wherein the therapeutic bacterial composition is substantially depleted of a residual habitat product of a fecal material.
 145. The method of claim 129, wherein the therapeutic bacterial composition is provided as an oral finished pharmaceutical dosage form comprising at least 1×10⁴ colony forming units of the bacteria per dose of the composition and including at least one pharmaceutically acceptable carrier and wherein the oral finished pharmaceutical dosage form is a capsule, a tablet, or a powder.
 146. A composition for treating, preventing, or reducing the severity of a disorder selected from the group consisting of Clostridium difficile infection and ulcerative colitis in a mammalian subject, the composition comprising a plurality of isolated bacteria or a purified bacterial preparation, wherein the plurality of isolated bacteria or the purified bacterial preparation comprises: (a) a Coprococcus comes, an Eubacterium rectale, and a Roseburia inulinivorans; or (b) a first bacterial operational taxonomic units (OTU) comprising a 16S rDNA comprising a sequence at least 97% identical to SEQ ID NO: 674, a second bacterial OTU comprising a 16S rDNA comprising a sequence at least 97% identical to SEQ ID NO: 856, and a third bacterial OTU comprising a 16S rDNA comprising a sequence at least 97% identical to SEQ ID NO:
 1639. 